full wwpdb em model validation report i · 2020-03-03 · page3 fullwwpdbemmodelvalidationreport...

Full wwPDB EM Model Validation Report i○

Mar 3, 2020 – 11:47 AM EST

PDB ID : 6M18EMDB ID : EMD-30040

Title : ACE2-B0AT1 complexAuthors : Yan, R.H.; Zhang, Y.Y.; Li, Y.N.; Xia, L.; Zhou, Q.

Deposited on : 2020-02-25Resolution : 2.90 Å(reported)

This is a Full wwPDB EM Model Validation Report for a publicly released PDB/EMDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith specific help available everywhere you see the i○ symbol.

The following versions of software and data (see references i○) were used in the production of this report:

MolProbity : 4.02b-467Mogul : 1.8.0 (224370), CSD as540be (2019)

buster-report : 1.1.7 (2018)Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)

Validation Pipeline (wwPDB-VP) : 2.8

https://www.wwpdb.org/validation/2017/EMValidationReportHelp



https://www.wwpdb.org/validation/2017/EMValidationReportHelp#references

Full wwPDB EM Model Validation Report 6M18

1 Overall quality at a glance i○

The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY

The reported resolution of this entry is 2.90 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

Metric Whole archive(#Entries)

EM structures(#Entries)

Clashscore 136327 1886Ramachandran outliers 132723 1663

Sidechain outliers 132532 1531

The table below summarises the geometric issues observed across the polymeric chains and theirfit to the map. The red, orange, yellow and green segments on the bar indicate the fraction ofresidues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively.A grey segment represents the fraction of residues that are not modelled. The numeric valuefor each fraction is indicated below the corresponding segment, with a dot representing fractions<=5%

Mol Chain Length Quality of chain

1 A 654

1 C 654

2 B 814

2 D 814

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#overall_quality


2 Entry composition i○

There are 6 unique types of molecules in this entry. The entry contains 22534 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the AltConf column contains the number of residues with at least one atomin alternate conformation and the Trace column contains the number of residues modelled with atmost 2 atoms.

• Molecule 1 is a protein called Sodium-dependent neutral amino acid transporter B(0)AT1.

Mol Chain Residues Atoms AltConf Trace

1 A 605 Total C N O S4794 3169 744 851 30 0 0

1 C 605 Total C N O S4794 3169 744 851 30 0 0

There are 42 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA -19 MET - initiating methionine UNP Q695T7A -18 ALA - expression tag UNP Q695T7A -17 ASP - expression tag UNP Q695T7A -16 TYR - expression tag UNP Q695T7A -15 LYS - expression tag UNP Q695T7A -14 ASP - expression tag UNP Q695T7A -13 ASP - expression tag UNP Q695T7A -12 ASP - expression tag UNP Q695T7A -11 ASP - expression tag UNP Q695T7A -10 LYS - expression tag UNP Q695T7A -9 SER - expression tag UNP Q695T7A -8 GLY - expression tag UNP Q695T7A -7 PRO - expression tag UNP Q695T7A -6 ASP - expression tag UNP Q695T7A -5 GLU - expression tag UNP Q695T7A -4 VAL - expression tag UNP Q695T7A -3 ASP - expression tag UNP Q695T7A -2 ALA - expression tag UNP Q695T7A -1 SER - expression tag UNP Q695T7A 0 GLY - expression tag UNP Q695T7A 1 ARG - expression tag UNP Q695T7C -19 MET - initiating methionine UNP Q695T7C -18 ALA - expression tag UNP Q695T7C -17 ASP - expression tag UNP Q695T7C -16 TYR - expression tag UNP Q695T7C -15 LYS - expression tag UNP Q695T7

Continued on next page...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#entry_composition


Continued from previous page...Chain Residue Modelled Actual Comment Reference

C -14 ASP - expression tag UNP Q695T7C -13 ASP - expression tag UNP Q695T7C -12 ASP - expression tag UNP Q695T7C -11 ASP - expression tag UNP Q695T7C -10 LYS - expression tag UNP Q695T7C -9 SER - expression tag UNP Q695T7C -8 GLY - expression tag UNP Q695T7C -7 PRO - expression tag UNP Q695T7C -6 ASP - expression tag UNP Q695T7C -5 GLU - expression tag UNP Q695T7C -4 VAL - expression tag UNP Q695T7C -3 ASP - expression tag UNP Q695T7C -2 ALA - expression tag UNP Q695T7C -1 SER - expression tag UNP Q695T7C 0 GLY - expression tag UNP Q695T7C 1 ARG - expression tag UNP Q695T7

• Molecule 2 is a protein called Angiotensin-converting enzyme 2.

Mol Chain Residues Atoms AltConf Trace

2 B 749 Total C N O S6095 3910 1018 1133 34 0 0

2 D 749 Total C N O S6095 3910 1018 1133 34 0 0

There are 20 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceB -8 MET - initiating methionine UNP Q9BYF1B -7 ARG - expression tag UNP Q9BYF1B 10 TRP - insertion UNP Q9BYF1B 11 SER - insertion UNP Q9BYF1B 12 HIS - insertion UNP Q9BYF1B 13 PRO - insertion UNP Q9BYF1B 14 GLN - insertion UNP Q9BYF1B 15 PHE - insertion UNP Q9BYF1B 16 GLU - insertion UNP Q9BYF1B 17 LYS - insertion UNP Q9BYF1D -8 MET - initiating methionine UNP Q9BYF1D -7 ARG - expression tag UNP Q9BYF1D 10 TRP - insertion UNP Q9BYF1D 11 SER - insertion UNP Q9BYF1



Continued from previous page...Chain Residue Modelled Actual Comment Reference

D 12 HIS - insertion UNP Q9BYF1D 13 PRO - insertion UNP Q9BYF1D 14 GLN - insertion UNP Q9BYF1D 15 PHE - insertion UNP Q9BYF1D 16 GLU - insertion UNP Q9BYF1D 17 LYS - insertion UNP Q9BYF1

• Molecule 3 is N-ACETYL-D-GLUCOSAMINE (three-letter code: NAG) (formula: C8H15NO6).

Mol Chain Residues Atoms AltConf

3 A 1 Total C N O84 48 6 30 0

3 A 1 Total C N O84 48 6 30 0

3 A 1 Total C N O84 48 6 30 0

3 A 1 Total C N O84 48 6 30 0

3 A 1 Total C N O84 48 6 30 0

3 A 1 Total C N O84 48 6 30 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0



Continued from previous page...Mol Chain Residues Atoms AltConf

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 B 1 Total C N O182 104 13 65 0

3 C 1 Total C N O84 48 6 30 0

3 C 1 Total C N O84 48 6 30 0

3 C 1 Total C N O84 48 6 30 0

3 C 1 Total C N O84 48 6 30 0

3 C 1 Total C N O84 48 6 30 0

3 C 1 Total C N O84 48 6 30 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0




3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

3 D 1 Total C N O182 104 13 65 0

• Molecule 4 is 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE (three-letter code: 3PH)(formula: C39H77O8P).


4 A 1 Total C O P96 78 16 2 0

4 A 1 Total C O P96 78 16 2 0




4 C 1 Total C O P96 78 16 2 0

4 C 1 Total C O P96 78 16 2 0

• Molecule 5 is ZINC ION (three-letter code: ZN) (formula: Zn).


5 B 1 Total Zn1 1 0

5 D 1 Total Zn1 1 0

• Molecule 6 is water.


6 A 10 Total O10 10 0

6 B 5 Total O5 5 0

6 C 10 Total O10 10 0

6 D 5 Total O5 5 0


3 Residue-property plots i○

These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometry. Residues are color-coded according to the number of geometric quality criteria for which they contain at least oneoutlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutiveresidues without any outlier are shown as a green connector. Residues present in the sample, butnot in the model, are shown in grey.

• Molecule 1: Sodium-dependent neutral amino acid transporter B(0)AT1

Chain A:

MET

ALA

ASP

TYR

LYS

ASP

ASP

ASP

ASP

LYS

SER

GLY

PRO

ASP

GLU

VAL

ASP

ALA

SER

GLY

ARG

VAL

ARG

LEU

V5 L6 P7 N8 R14

S17

L18

A19

E20

L21

E22

T23

I24

E25

Q26

E27

E28

R32

K38

G51

L52

G53

W56

R57

L75

I76

L77

L78

V79

L80

E81

G82

I83

P84

L85

R97

S105

L111

K112

G113

L114

L120

Y129

L181

N182

I183

W205

S206

I213

T219

V223

Y224

I225

T226

L229

P230

Y231

V232

V233

L234

T235

I236

F237

L238

E261

L262

A263

Q264

W268

Q274

S278

F289

S290

S291

V295

H296

N297

S307

V317

Q331

R332

Y333

D334

D335

C336

F337

I341

L350

P351

N354

V355

T356

Q357

E358

V361

Q364

C383

F388

V393

L398

V402

K409

L427

S430

M436

E437

G438

V439

V440

V441

P442

L443

L461

I462

C463

L464

G465

T466

I497

M502

V508

V511

F520

H524

W530

R535

K572

S573

Y583

V584

V585

V586

V587

I588

V589

A590

G591

V592

P593

S594

L595

T596

I597

P598

G599

Y600

K604

L605

H609

CYS

GLN

LYS

PRO

GLY

ASP

HIS

GLN

GLY

LEU

VAL

SER

THR

LEU

SER

THR

ALA

SER

MET

ASN

GLY

ASP

LEU

LYS

TYR

• Molecule 1: Sodium-dependent neutral amino acid transporter B(0)AT1

Chain C:

MET

ALA

ASP

TYR

LYS

ASP

ASP

ASP

ASP

LYS

SER

GLY

PRO

ASP

GLU

VAL

ASP

ALA

SER

GLY

ARG

VAL

ARG

LEU

V5 L6 P7 N8 R14

S17

L18

A19

E20

L21

E22

T23

I24

E25

Q26

E27

E28

R32

K38

G51

L52

G53

W56

R57

L75

I76

L77

L78

V79

L80

E81

G82

I83

P84

L85

R97

S105

L111

K112

G113

L114

L120

Y129

L181

N182

I183

W205

S206

I213

T219

V223

Y224

I225

T226

L229

P230

Y231

V232

V233

L234

T235

I236

F237

L238

E261

L262

A263

Q264

W268

Q274

S278

F289

S290

S291

V295

H296

N297

S307

V317

Q331

R332

Y333

D334

D335

C336

F337

I341

L350

P351

N354

V355

T356

Q357

E358

V361

Q364

C383

F388

V393

L398

V402

K409

L427

S430

M436

E437

G438

V439

V440

V441

P442

L443

L461

I462

C463

L464

G465

T466

I497

M502

V508

V511

F520

H524

W530

T533

W534

R535

V536

V537

K572

S573

Y578

V582

Y583

V584

V587

I588

V589

A590

G591

V592

P593

S594

L595

T596

I597

P598

G599

Y600

K604

L605

H609

CYS

GLN

LYS

PRO

GLY

ASP

HIS

GLN

GLY

LEU

VAL

SER

THR

LEU

SER

THR

ALA

SER

MET

ASN

GLY

ASP

LEU

LYS

TYR

• Molecule 2: Angiotensin-converting enzyme 2

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#residue_plots


Chain B:ME

TAR

GSE

RSE

RSE

RSE

RTR

PLE

ULE

ULE

USE

RLE

UVA

LAL

AVA

LTH

RAL

AAL

ATR

PSE

RHI

SPR

OGL

NPH

EGL

ULY

SGL

NSE

RT2

0I2

1

L45

A46

S47

W48

N49

Y50

N51

T52

N53

I54

T55

E56

V59

Q60

N63

P84

L85

N90

V93

Q98

N103

S109

K112

K131

V132

C133

Y183

N194

Y243

K247

W302

I307

K341

A342

V343

C344

L359

D367

K476

D509

S611

A614

K619

I622

R644

E667

R678

I679

S680

P696

E699

S709

R716

L725

P738

V739

V749

M750

G751

V752

I753

V754

V755

G756

I757

V758

I759

L760

I761

R768

LYS

LYS

LYS

ASN

LYS

ALA

ARG

SER

GLY

GLU

ASN

PRO

TYR

ALA

SER

ILE

ASP

ILE

SER

LYS

GLY

GLU

ASN

ASN

PRO

GLY

PHE

GLN

ASN

THR

ASP

ASP

VAL

GLN

THR

SER

PHE

• Molecule 2: Angiotensin-converting enzyme 2

Chain D:

MET

ARG

SER

SER

SER

SER

TRP

LEU

LEU

LEU

SER

LEU

VAL

ALA

VAL

THR

ALA

ALA

TRP

SER

HIS

PRO

GLN

PHE

GLU

LYS

GLN

SER

T20

I21

L45

A46

S47

W48

N49

Y50

N51

T52

N53

I54

T55

E56

V59

Q60

N61

M62

N63

G66

P84

L85

N90

V93

Q98

N103

S109

K112

C133

D136

Y183

N194

Y243

K247

W302

I307

K341

A342

V343

C344

L359

D367

D509

I513

S611

A614

K619

I622

R644

E667

P677

R678

I679

S680

P696

E699

S709

R716

L725

P738

V739

V749

M750

G751

V752

I753

V754

V755

G756

I757

V758

I759

L760

I761

R768

LYS

LYS

LYS

ASN

LYS

ALA

ARG

SER

GLY

GLU

ASN

PRO

TYR

ALA

SER

ILE

ASP

ILE

SER

LYS

GLY

GLU

ASN

ASN

PRO

GLY

PHE

GLN

ASN

THR

ASP

ASP

VAL

GLN

THR

SER

PHE


4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C2 DepositorNumber of particles used 418140 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE

CORRECTIONDepositor

Microscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2

) 50 DepositorMinimum defocus (nm) Not provided DepositorMaximum defocus (nm) Not provided DepositorMagnification Not provided DepositorImage detector GATAN K3 BIOQUANTUM (6k x 4k) Depositor

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info


5 Model quality i○

5.1 Standard geometry i○

Bond lengths and bond angles in the following residue types are not validated in this section: 3PH,ZN, NAG

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.47 0/4934 0.63 0/67401 C 0.47 0/4934 0.63 0/67402 B 0.34 0/6258 0.51 0/84962 D 0.34 0/6258 0.51 0/8496All All 0.41 0/22384 0.57 0/30472

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no planarity outliers.

5.2 Too-close contacts i○

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 4794 0 4748 145 01 C 4794 0 4748 145 02 B 6095 0 5907 44 02 D 6095 0 5907 46 03 A 84 0 76 0 03 B 182 0 163 0 03 C 84 0 76 0 03 D 182 0 163 0 04 A 96 0 150 1 0


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#model_quality

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#standard_geometry

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts


Continued from previous page...Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes4 C 96 0 150 0 05 B 1 0 0 0 05 D 1 0 0 0 06 A 10 0 0 0 06 B 5 0 0 0 06 C 10 0 0 0 06 D 5 0 0 0 0All All 22534 0 22088 377 0

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 8.

All (377) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:85:LEU:HD22 1:A:502:MET:CE 1.70 1.211:C:85:LEU:HD22 1:C:502:MET:CE 1.70 1.201:C:592:VAL:O 1:C:596:THR:HG23 1.44 1.151:A:584:VAL:O 1:A:588:ILE:HG23 1.43 1.151:A:592:VAL:O 1:A:596:THR:HG23 1.44 1.151:C:584:VAL:O 1:C:588:ILE:HG23 1.43 1.15

1:A:331:GLN:HG2 1:A:409:LYS:HE3 1.33 1.111:A:85:LEU:HD22 1:A:502:MET:HE3 1.30 1.091:C:331:GLN:HG2 1:C:409:LYS:HE3 1.33 1.051:C:85:LEU:HD22 1:C:502:MET:HE1 1.37 1.021:A:331:GLN:HG2 1:A:409:LYS:CE 1.90 1.011:C:331:GLN:HG2 1:C:409:LYS:CE 1.90 0.991:C:85:LEU:HD22 1:C:502:MET:HE3 1.42 0.981:C:583:TYR:O 1:C:587:VAL:HG23 1.66 0.961:A:583:TYR:O 1:A:587:VAL:HG23 1.66 0.94

1:A:85:LEU:HD22 1:A:502:MET:HE1 1.48 0.931:A:226:THR:O 1:A:230:PRO:HD3 1.72 0.901:A:226:THR:O 1:A:230:PRO:CD 2.20 0.901:C:226:THR:O 1:C:230:PRO:HD3 1.72 0.901:C:226:THR:O 1:C:230:PRO:CD 2.20 0.89

1:A:21:LEU:HD22 1:A:24:ILE:HG21 1.54 0.891:C:85:LEU:CD2 1:C:502:MET:CE 2.51 0.891:C:21:LEU:HD22 1:C:24:ILE:HG21 1.54 0.881:A:85:LEU:CD2 1:A:502:MET:HE3 2.04 0.881:A:85:LEU:CD2 1:A:502:MET:CE 2.51 0.871:A:597:ILE:HB 1:A:598:PRO:HD3 1.56 0.87



Continued from previous page...


Clashoverlap (Å)

1:A:79:VAL:O 1:A:80:LEU:HD23 1.75 0.871:C:79:VAL:O 1:C:80:LEU:HD23 1.75 0.861:C:597:ILE:HB 1:C:598:PRO:HD3 1.56 0.861:A:17:SER:HB3 1:A:20:GLU:HG2 1.58 0.861:C:219:THR:O 1:C:223:VAL:HG13 1.78 0.831:A:331:GLN:CG 1:A:409:LYS:HE3 2.08 0.831:C:17:SER:HB3 1:C:20:GLU:HG2 1.58 0.831:A:219:THR:O 1:A:223:VAL:HG13 1.78 0.83

1:A:226:THR:HG21 1:A:430:SER:HB3 1.61 0.831:A:21:LEU:CD2 1:A:24:ILE:HG21 2.09 0.821:A:592:VAL:O 1:A:596:THR:CG2 2.28 0.821:C:331:GLN:CG 1:C:409:LYS:HE3 2.08 0.82

1:C:226:THR:HG21 1:C:430:SER:HB3 1.61 0.811:C:21:LEU:CD2 1:C:24:ILE:HG21 2.09 0.811:C:85:LEU:CD2 1:C:502:MET:HE1 2.12 0.791:A:589:VAL:O 1:A:593:PRO:HD2 1.82 0.791:C:589:VAL:O 1:C:593:PRO:HD2 1.82 0.791:C:583:TYR:O 1:C:587:VAL:CG2 2.30 0.791:C:592:VAL:O 1:C:596:THR:CG2 2.28 0.791:A:583:TYR:O 1:A:587:VAL:CG2 2.30 0.782:D:757:ILE:O 2:D:761:ILE:HG23 1.85 0.762:B:757:ILE:O 2:B:761:ILE:HG23 1.85 0.76

1:A:213:ILE:HG21 2:B:760:LEU:HD13 1.69 0.751:C:213:ILE:HG21 2:D:760:LEU:HD13 1.69 0.751:C:436:MET:O 1:C:436:MET:HG3 1.87 0.741:C:597:ILE:HB 1:C:598:PRO:CD 2.18 0.731:C:226:THR:O 1:C:230:PRO:HD2 1.88 0.721:A:597:ILE:HB 1:A:598:PRO:CD 2.18 0.72

1:A:589:VAL:HG23 1:A:590:ALA:N 2.04 0.721:C:589:VAL:HG23 1:C:590:ALA:N 2.04 0.721:C:85:LEU:CD2 1:C:502:MET:HE3 2.16 0.721:A:226:THR:O 1:A:230:PRO:HD2 1.88 0.722:D:622:ILE:HB 2:D:679:ILE:CG2 2.19 0.722:B:622:ILE:HB 2:B:679:ILE:CG2 2.19 0.721:A:436:MET:O 1:A:436:MET:HG3 1.87 0.72

1:A:332:ARG:HH21 1:A:388:PHE:HE1 1.37 0.711:A:230:PRO:O 1:A:234:LEU:HB2 1.92 0.701:C:262:LEU:O 1:C:264:GLN:N 2.23 0.701:C:230:PRO:O 1:C:234:LEU:HB2 1.92 0.70

1:A:21:LEU:HD22 1:A:24:ILE:CG2 2.22 0.691:C:21:LEU:O 1:C:23:THR:N 2.26 0.69





Clashoverlap (Å)

1:A:21:LEU:O 1:A:23:THR:N 2.26 0.691:A:589:VAL:HG23 1:A:590:ALA:H 1.57 0.691:A:332:ARG:NH2 1:A:388:PHE:CE1 2.60 0.691:C:21:LEU:C 1:C:23:THR:H 1.96 0.69

1:C:332:ARG:NH2 1:C:388:PHE:CE1 2.60 0.691:C:21:LEU:HD22 1:C:24:ILE:CG2 2.22 0.681:C:589:VAL:HG23 1:C:590:ALA:H 1.57 0.681:C:332:ARG:HH21 1:C:388:PHE:HE1 1.37 0.68

1:A:21:LEU:C 1:A:23:THR:H 1.96 0.681:A:350:LEU:O 1:A:351:PRO:O 2.12 0.68

1:A:356:THR:OG1 1:A:357:GLN:N 2.27 0.671:A:588:ILE:HD12 1:A:589:VAL:N 2.10 0.671:A:83:ILE:CD1 1:A:307:SER:CB 2.73 0.671:C:350:LEU:O 1:C:351:PRO:O 2.12 0.66

1:C:205:TRP:CZ2 1:C:466:THR:CG2 2.79 0.661:C:588:ILE:HD12 1:C:589:VAL:N 2.10 0.661:A:205:TRP:CZ2 1:A:466:THR:CG2 2.79 0.651:A:85:LEU:CD2 1:A:502:MET:HE1 2.24 0.651:C:83:ILE:CD1 1:C:307:SER:CB 2.73 0.65

1:A:332:ARG:NH2 1:A:388:PHE:CD1 2.65 0.651:C:38:LYS:HE3 1:C:297:ASN:HD21 1.62 0.65

1:C:592:VAL:HG12 1:C:593:PRO:HD3 1.79 0.651:A:588:ILE:HG13 1:A:589:VAL:H 1.62 0.641:A:262:LEU:O 1:A:264:GLN:N 2.23 0.641:A:38:LYS:HE3 1:A:297:ASN:HD21 1.62 0.64

1:A:592:VAL:HG12 1:A:593:PRO:HD3 1.79 0.641:C:332:ARG:NH2 1:C:388:PHE:CD1 2.65 0.641:C:588:ILE:HG13 1:C:589:VAL:H 1.62 0.641:A:21:LEU:O 1:A:24:ILE:HG22 1.98 0.631:C:21:LEU:O 1:C:24:ILE:HG22 1.98 0.632:D:622:ILE:HB 2:D:679:ILE:HG21 1.80 0.632:D:752:VAL:O 2:D:755:VAL:HG12 1.99 0.63

1:C:356:THR:OG1 1:C:357:GLN:N 2.27 0.622:B:752:VAL:O 2:B:755:VAL:HG12 1.99 0.622:D:751:GLY:O 2:D:754:VAL:HG22 1.99 0.622:B:622:ILE:HB 2:B:679:ILE:HG21 1.80 0.612:B:751:GLY:O 2:B:754:VAL:HG22 1.99 0.611:C:83:ILE:HD11 1:C:307:SER:OG 2.01 0.611:A:53:GLY:O 1:A:57:ARG:HB3 2.01 0.60

2:D:619:LYS:HD3 2:D:725:LEU:HD22 1.83 0.601:A:331:GLN:HA 1:A:331:GLN:OE1 2.02 0.60





Clashoverlap (Å)

1:C:53:GLY:O 1:C:57:ARG:HB3 2.01 0.601:C:595:LEU:O 1:C:598:PRO:HD2 2.01 0.601:C:83:ILE:CD1 1:C:307:SER:OG 2.50 0.60

1:A:443:LEU:HD23 1:A:462:ILE:HD11 1.84 0.601:A:595:LEU:O 1:A:598:PRO:HD2 2.01 0.601:C:6:LEU:HB3 1:C:7:PRO:HD2 1.85 0.591:A:83:ILE:CD1 1:A:307:SER:OG 2.50 0.591:A:83:ILE:HD11 1:A:307:SER:OG 2.01 0.591:A:511:VAL:HG11 1:A:535:ARG:HE 1.67 0.592:D:622:ILE:HB 2:D:679:ILE:HG22 1.85 0.591:A:6:LEU:HB3 1:A:7:PRO:HD2 1.85 0.591:C:6:LEU:HB3 1:C:7:PRO:CD 2.32 0.592:B:619:LYS:HD3 2:B:725:LEU:HD22 1.83 0.591:A:24:ILE:O 1:A:27:GLU:HG3 2.03 0.58

1:C:331:GLN:OE1 1:C:331:GLN:HA 2.02 0.581:C:443:LEU:HD23 1:C:462:ILE:HD11 1.84 0.581:A:355:VAL:O 1:A:355:VAL:HG12 2.03 0.581:A:6:LEU:HB3 1:A:7:PRO:CD 2.32 0.581:A:28:GLU:OE2 1:A:97:ARG:NH1 2.36 0.581:C:355:VAL:O 1:C:355:VAL:HG12 2.03 0.58

1:C:356:THR:HG23 1:C:358:GLU:HG3 1.85 0.581:C:24:ILE:O 1:C:27:GLU:HG3 2.03 0.58

1:C:56:TRP:HA 1:C:398:LEU:HD23 1.86 0.581:C:28:GLU:OE2 1:C:97:ARG:NH1 2.36 0.581:C:21:LEU:C 1:C:23:THR:N 2.58 0.57

1:C:511:VAL:HG11 1:C:535:ARG:HE 1.67 0.572:D:749:VAL:O 2:D:752:VAL:HG22 2.04 0.57

1:C:205:TRP:CZ2 1:C:466:THR:HG21 2.40 0.572:B:622:ILE:HB 2:B:679:ILE:HG22 1.85 0.57

1:A:356:THR:HG23 1:A:358:GLU:HG3 1.85 0.571:A:226:THR:CG2 1:A:430:SER:HB3 2.33 0.571:C:226:THR:CG2 1:C:430:SER:HB3 2.33 0.572:D:611:SER:HB3 2:D:614:ALA:HB2 1.86 0.571:A:21:LEU:C 1:A:23:THR:N 2.58 0.57

1:C:51:GLY:HA2 1:C:427:LEU:HG 1.87 0.571:A:51:GLY:HA2 1:A:427:LEU:HG 1.87 0.572:B:749:VAL:O 2:B:752:VAL:HG22 2.04 0.56

2:D:644:ARG:NH1 2:D:667:GLU:OE1 2.38 0.562:D:341:LYS:O 2:D:342:ALA:HB2 2.05 0.561:A:56:TRP:HA 1:A:398:LEU:HD23 1.86 0.562:B:85:LEU:HD21 2:B:98:GLN:HG2 1.86 0.56





Clashoverlap (Å)

2:D:85:LEU:HD21 2:D:98:GLN:HG2 1.86 0.562:B:678:ARG:O 2:B:679:ILE:HB 2.06 0.562:B:611:SER:HB3 2:B:614:ALA:HB2 1.86 0.561:A:205:TRP:CZ2 1:A:466:THR:HG21 2.40 0.562:B:644:ARG:NH1 2:B:667:GLU:OE1 2.38 0.561:A:17:SER:CB 1:A:20:GLU:HG2 2.33 0.551:C:25:GLU:HA 1:C:28:GLU:HG2 1.88 0.552:B:341:LYS:O 2:B:342:ALA:HB2 2.05 0.552:D:678:ARG:O 2:D:679:ILE:HB 2.06 0.55

1:C:393:VAL:HG11 1:C:402:VAL:HG21 1.89 0.551:A:393:VAL:HG11 1:A:402:VAL:HG21 1.89 0.541:A:25:GLU:HA 1:A:28:GLU:HG2 1.88 0.541:C:18:LEU:CD1 1:C:520:PHE:CD2 2.91 0.541:A:18:LEU:CD1 1:A:520:PHE:CD2 2.91 0.541:C:21:LEU:CD2 1:C:24:ILE:CG2 2.83 0.541:C:274:GLN:O 1:C:278:SER:N 2.38 0.541:C:17:SER:CB 1:C:20:GLU:HG2 2.33 0.541:A:597:ILE:CB 1:A:598:PRO:HD3 2.35 0.532:D:103:ASN:HB2 2:D:194:ASN:HD21 1.73 0.531:A:181:LEU:O 1:A:182:ASN:HB3 2.08 0.53

1:C:592:VAL:HG12 1:C:593:PRO:CD 2.38 0.531:A:592:VAL:HG12 1:A:593:PRO:CD 2.38 0.531:A:83:ILE:HB 1:A:84:PRO:HD3 1.91 0.53

2:B:103:ASN:HB2 2:B:194:ASN:HD21 1.73 0.531:C:588:ILE:CG1 1:C:589:VAL:N 2.72 0.531:C:77:LEU:O 1:C:81:GLU:HG2 2.09 0.531:A:8:ASN:ND2 1:A:508:VAL:O 2.42 0.531:C:8:ASN:ND2 1:C:508:VAL:O 2.42 0.531:A:572:LYS:HG3 1:A:573:SER:H 1.74 0.531:A:77:LEU:O 1:A:81:GLU:HG2 2.09 0.531:C:83:ILE:HB 1:C:84:PRO:HD3 1.91 0.531:C:181:LEU:O 1:C:182:ASN:HB3 2.08 0.521:C:588:ILE:CD1 1:C:589:VAL:N 2.73 0.521:C:589:VAL:CG2 1:C:590:ALA:N 2.73 0.521:A:592:VAL:HB 1:A:593:PRO:HD2 1.92 0.521:A:274:GLN:O 1:A:278:SER:N 2.38 0.521:A:588:ILE:CG1 1:A:589:VAL:N 2.72 0.521:C:18:LEU:HD12 1:C:520:PHE:CD2 2.44 0.521:A:18:LEU:HD12 1:A:520:PHE:CD2 2.44 0.521:C:592:VAL:HB 1:C:593:PRO:HD2 1.92 0.522:D:47:SER:O 2:D:51:ASN:ND2 2.41 0.52





Clashoverlap (Å)

1:A:337:PHE:CD2 1:A:357:GLN:OE1 2.63 0.521:C:337:PHE:CD2 1:C:357:GLN:OE1 2.63 0.521:C:524:HIS:ND1 1:C:524:HIS:O 2.43 0.511:A:588:ILE:CD1 1:A:589:VAL:N 2.73 0.511:C:572:LYS:HG3 1:C:573:SER:H 1.74 0.511:A:112:LYS:HD3 1:A:600:TYR:CZ 2.46 0.512:B:47:SER:O 2:B:51:ASN:ND2 2.41 0.51

1:C:112:LYS:HD3 1:C:600:TYR:CZ 2.46 0.511:A:589:VAL:CG2 1:A:590:ALA:N 2.73 0.511:A:588:ILE:O 1:A:592:VAL:HG23 2.11 0.51

1:A:524:HIS:ND1 1:A:524:HIS:O 2.43 0.511:A:589:VAL:CG2 1:A:590:ALA:H 2.24 0.501:C:588:ILE:O 1:C:592:VAL:HG23 2.11 0.501:C:6:LEU:CB 1:C:7:PRO:CD 2.88 0.502:D:45:LEU:O 2:D:49:ASN:ND2 2.44 0.50

1:A:21:LEU:CD2 1:A:24:ILE:CG2 2.83 0.501:A:592:VAL:HB 1:A:593:PRO:CD 2.42 0.501:C:592:VAL:HB 1:C:593:PRO:CD 2.42 0.502:B:45:LEU:O 2:B:49:ASN:ND2 2.44 0.501:C:597:ILE:CB 1:C:598:PRO:CD 2.89 0.502:D:20:THR:O 2:D:20:THR:OG1 2.29 0.501:A:6:LEU:CB 1:A:7:PRO:CD 2.88 0.49

2:D:759:ILE:HG22 2:D:759:ILE:O 2.12 0.491:A:205:TRP:CZ2 1:A:466:THR:HG22 2.46 0.491:C:439:VAL:O 1:C:439:VAL:HG12 2.12 0.49

1:C:205:TRP:CZ2 1:C:466:THR:HG22 2.46 0.491:C:597:ILE:CB 1:C:598:PRO:HD3 2.35 0.49

1:A:439:VAL:HG12 1:A:439:VAL:O 2.12 0.482:B:759:ILE:O 2:B:759:ILE:HG22 2.12 0.48

1:C:437:GLU:HA 1:C:437:GLU:OE1 2.14 0.481:C:105:SER:HB2 1:C:112:LYS:HG3 1.95 0.481:C:26:GLN:N 1:C:26:GLN:OE1 2.47 0.48

2:D:302:TRP:HE3 2:D:307:ILE:HG22 1.78 0.481:A:597:ILE:CB 1:A:598:PRO:CD 2.89 0.481:A:105:SER:HB2 1:A:112:LYS:HG3 1.95 0.482:B:302:TRP:HE3 2:B:307:ILE:HG22 1.78 0.482:B:52:THR:O 2:B:342:ALA:HB2 2.14 0.481:A:26:GLN:N 1:A:26:GLN:OE1 2.47 0.48

1:A:588:ILE:HG13 1:A:589:VAL:N 2.28 0.481:C:21:LEU:HA 1:C:21:LEU:HD23 1.79 0.482:D:52:THR:O 2:D:342:ALA:HB2 2.14 0.48





Clashoverlap (Å)

1:A:437:GLU:OE1 1:A:437:GLU:HA 2.14 0.471:C:233:VAL:O 1:C:233:VAL:HG12 2.15 0.471:C:588:ILE:CG1 1:C:589:VAL:H 2.27 0.471:A:331:GLN:CG 1:A:409:LYS:CE 2.77 0.471:A:331:GLN:HG2 1:A:409:LYS:NZ 2.30 0.472:B:54:ILE:HG12 2:B:342:ALA:HA 1.97 0.471:C:588:ILE:HG13 1:C:589:VAL:N 2.28 0.471:C:589:VAL:CG2 1:C:590:ALA:H 2.24 0.471:C:79:VAL:HG23 1:C:79:VAL:O 2.14 0.472:B:20:THR:OG1 2:B:20:THR:O 2.29 0.471:A:111:LEU:O 1:A:113:GLY:N 2.40 0.461:A:354:ASN:N 1:A:354:ASN:OD1 2.41 0.461:A:79:VAL:O 1:A:79:VAL:HG23 2.14 0.461:C:583:TYR:O 1:C:587:VAL:CB 2.64 0.46

1:A:233:VAL:HG12 1:A:233:VAL:O 2.15 0.462:B:679:ILE:O 2:B:679:ILE:HG22 2.15 0.46

1:C:25:GLU:HG3 1:C:295:VAL:HG23 1.97 0.461:C:331:GLN:HG2 1:C:409:LYS:NZ 2.30 0.462:D:754:VAL:HG23 2:D:755:VAL:N 2.31 0.461:A:83:ILE:HG22 1:A:530:TRP:CH2 2.51 0.462:D:679:ILE:O 2:D:679:ILE:HG22 2.15 0.46

1:A:25:GLU:HG3 1:A:295:VAL:HG23 1.97 0.462:D:54:ILE:HG12 2:D:342:ALA:HA 1.97 0.461:A:583:TYR:O 1:A:587:VAL:CB 2.64 0.462:B:709:SER:OG 2:D:716:ARG:NH1 2.49 0.462:B:678:ARG:HG3 2:B:678:ARG:O 2.16 0.461:C:111:LEU:O 1:C:113:GLY:N 2.40 0.462:D:183:TYR:OH 2:D:509:ASP:OD1 2.32 0.461:C:341:ILE:HG23 1:C:355:VAL:HG12 1.99 0.451:C:83:ILE:HG22 1:C:530:TRP:CH2 2.51 0.451:C:229:LEU:O 1:C:231:TYR:N 2.50 0.452:B:60:GLN:HA 2:B:63:ASN:HB2 1.98 0.451:A:229:LEU:HB3 1:A:230:PRO:HD3 1.99 0.451:A:25:GLU:C 1:A:27:GLU:H 2.20 0.45

1:A:56:TRP:CD1 1:A:56:TRP:C 2.90 0.452:B:754:VAL:HG23 2:B:755:VAL:N 2.31 0.45

1:C:25:GLU:C 1:C:27:GLU:H 2.20 0.452:B:716:ARG:NH1 2:D:709:SER:OG 2.49 0.451:A:56:TRP:O 1:A:56:TRP:CD1 2.70 0.44

2:B:183:TYR:OH 2:B:509:ASP:OD1 2.32 0.442:D:678:ARG:O 2:D:678:ARG:HG3 2.16 0.44





Clashoverlap (Å)

1:C:56:TRP:CD1 1:C:56:TRP:C 2.90 0.442:D:60:GLN:HA 2:D:63:ASN:HB2 1.98 0.44

1:A:341:ILE:HG23 1:A:355:VAL:HG12 1.99 0.441:C:32:ARG:NH2 1:C:291:SER:O 2.51 0.441:A:32:ARG:NH2 1:A:291:SER:O 2.51 0.442:D:752:VAL:HG23 2:D:753:ILE:N 2.31 0.441:A:229:LEU:O 1:A:231:TYR:N 2.50 0.441:C:238:LEU:O 1:C:238:LEU:HD12 2.18 0.44

1:C:354:ASN:OD1 1:C:354:ASN:N 2.41 0.441:C:83:ILE:HD11 1:C:307:SER:CB 2.46 0.441:A:18:LEU:HD11 1:A:520:PHE:CD2 2.52 0.441:C:229:LEU:HB3 1:C:230:PRO:HD3 1.99 0.442:D:109:SER:HB3 2:D:112:LYS:HB2 2.00 0.441:C:56:TRP:CD1 1:C:56:TRP:O 2.70 0.441:A:17:SER:HB3 1:A:20:GLU:CG 2.40 0.441:A:262:LEU:C 1:A:264:GLN:H 2.16 0.44

2:B:752:VAL:HG23 2:B:753:ILE:N 2.31 0.441:A:441:VAL:HB 1:A:442:PRO:HD3 2.00 0.43

1:C:234:LEU:HD11 1:C:317:VAL:HG22 2.00 0.432:B:109:SER:HB3 2:B:112:LYS:HB2 2.00 0.431:C:262:LEU:C 1:C:264:GLN:H 2.16 0.43

2:D:696:PRO:HG2 2:D:699:GLU:HG3 2.00 0.431:A:238:LEU:HD12 1:A:238:LEU:O 2.18 0.432:D:760:LEU:HA 2:D:760:LEU:HD23 1.77 0.432:B:696:PRO:HG2 2:B:699:GLU:HG3 2.00 0.432:D:136:ASP:OD1 2:D:136:ASP:N 2.47 0.432:B:56:GLU:HA 2:B:59:VAL:HG23 2.01 0.431:C:441:VAL:HB 1:C:442:PRO:HD3 2.00 0.431:C:18:LEU:HD11 1:C:520:PHE:CD2 2.52 0.431:A:443:LEU:HA 1:A:443:LEU:HD12 1.86 0.432:D:56:GLU:HA 2:D:59:VAL:HG23 2.01 0.43

2:B:760:LEU:HD23 2:B:760:LEU:HA 1.77 0.431:C:443:LEU:HA 1:C:443:LEU:HD12 1.86 0.431:C:56:TRP:O 1:C:56:TRP:HD1 2.02 0.43

2:D:367:ASP:OD1 2:D:367:ASP:N 2.52 0.431:A:234:LEU:HD11 1:A:317:VAL:HG22 2.00 0.421:C:337:PHE:HD2 1:C:357:GLN:CD 2.22 0.421:C:229:LEU:C 1:C:231:TYR:N 2.73 0.421:A:235:THR:O 1:A:238:LEU:N 2.42 0.421:A:334:ASP:C 1:A:336:CYS:H 2.23 0.42

1:A:114:LEU:HD23 1:A:497:ILE:HG23 2.02 0.42Continued on next page...




Clashoverlap (Å)

1:C:592:VAL:CG1 1:C:593:PRO:HD3 2.47 0.421:A:337:PHE:HD2 1:A:357:GLN:CD 2.22 0.421:C:592:VAL:CB 1:C:593:PRO:CD 2.97 0.421:C:17:SER:HB3 1:C:20:GLU:CG 2.40 0.421:A:595:LEU:O 1:A:597:ILE:N 2.53 0.422:B:90:ASN:HB3 2:B:93:VAL:HG12 2.02 0.421:C:334:ASP:C 1:C:336:CYS:H 2.23 0.421:A:264:GLN:O 1:A:268:TRP:HD1 2.03 0.421:A:592:VAL:CB 1:A:593:PRO:CD 2.97 0.422:B:343:VAL:O 2:B:359:LEU:HD21 2.20 0.421:C:235:THR:C 1:C:237:PHE:N 2.73 0.42

1:C:114:LEU:HD23 1:C:497:ILE:HG23 2.02 0.422:D:343:VAL:O 2:D:359:LEU:HD21 2.20 0.421:A:262:LEU:C 1:A:264:GLN:N 2.73 0.42

1:A:592:VAL:CG1 1:A:593:PRO:HD3 2.47 0.421:A:235:THR:C 1:A:237:PHE:N 2.73 0.41

2:D:738:PRO:HG2 2:D:739:VAL:HG23 2.02 0.411:A:229:LEU:C 1:A:231:TYR:N 2.73 0.412:B:51:ASN:O 2:B:342:ALA:HB1 2.20 0.412:D:62:MET:O 2:D:66:GLY:N 2.49 0.41

1:A:443:LEU:CD2 1:A:462:ILE:HD11 2.50 0.414:A:708:3PH:H3E2 4:A:708:3PH:H3H1 1.88 0.412:B:21:ILE:HD11 2:B:84:PRO:HD2 2.03 0.412:B:476:LYS:HA 2:B:476:LYS:HD3 1.89 0.411:C:289:PHE:CE1 1:C:437:GLU:HG2 2.56 0.411:A:83:ILE:HG22 1:A:530:TRP:HH2 1.85 0.412:B:738:PRO:HG2 2:B:739:VAL:HG23 2.02 0.411:C:264:GLN:O 1:C:268:TRP:HD1 2.03 0.41

2:B:752:VAL:CG2 2:B:753:ILE:N 2.84 0.412:D:90:ASN:HB3 2:D:93:VAL:HG12 2.02 0.411:A:83:ILE:CG2 1:A:530:TRP:HH2 2.33 0.412:B:243:TYR:OH 2:B:247:LYS:NZ 2.53 0.411:A:336:CYS:SG 1:A:383:CYS:CB 3.07 0.411:C:83:ILE:HG22 1:C:530:TRP:HH2 1.85 0.411:A:25:GLU:HG3 1:A:295:VAL:CG2 2.51 0.411:C:350:LEU:C 1:C:351:PRO:O 2.59 0.412:D:51:ASN:O 2:D:342:ALA:HB1 2.20 0.411:A:18:LEU:HA 1:A:18:LEU:HD13 1.94 0.412:D:677:PRO:C 2:D:679:ILE:N 2.73 0.411:A:361:VAL:HA 1:A:364:GLN:HB2 2.03 0.411:A:18:LEU:HD12 1:A:520:PHE:CE2 2.56 0.41





Clashoverlap (Å)

1:C:578:TYR:HB3 1:C:582:VAL:HG11 2.03 0.411:C:595:LEU:O 1:C:597:ILE:N 2.53 0.411:A:350:LEU:C 1:A:351:PRO:O 2.59 0.402:B:131:LYS:HE2 2:B:131:LYS:HB3 1.82 0.401:C:229:LEU:C 1:C:231:TYR:H 2.24 0.401:C:336:CYS:SG 1:C:383:CYS:CB 3.07 0.401:C:18:LEU:HD12 1:C:520:PHE:CE2 2.56 0.401:A:56:TRP:O 1:A:56:TRP:HD1 2.02 0.402:B:367:ASP:N 2:B:367:ASP:OD1 2.52 0.401:C:361:VAL:HA 1:C:364:GLN:HB2 2.03 0.402:D:513:ILE:HD12 2:D:513:ILE:HA 1.95 0.401:A:289:PHE:CE1 1:A:437:GLU:HG2 2.56 0.401:A:586:VAL:O 1:A:589:VAL:HG22 2.22 0.401:C:262:LEU:C 1:C:264:GLN:N 2.73 0.401:C:533:THR:HA 1:C:537:VAL:HB 2.04 0.402:D:21:ILE:HD11 2:D:84:PRO:HD2 2.03 0.402:D:243:TYR:OH 2:D:247:LYS:NZ 2.53 0.401:C:235:THR:O 1:C:238:LEU:N 2.42 0.401:C:25:GLU:HG3 1:C:295:VAL:CG2 2.51 0.401:C:83:ILE:CG2 1:C:530:TRP:HH2 2.33 0.401:A:354:ASN:O 1:A:355:VAL:HB 2.22 0.401:A:6:LEU:HA 1:A:6:LEU:HD23 1.89 0.40

2:D:752:VAL:CG2 2:D:753:ILE:N 2.84 0.40

There are no symmetry-related clashes.

5.3 Torsion angles i○

5.3.1 Protein backbone i○

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 603/654 (92%) 506 (84%) 79 (13%) 18 (3%) 5 19

1 C 603/654 (92%) 506 (84%) 79 (13%) 18 (3%) 5 19Continued on next page...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_backbone


Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles

2 B 747/814 (92%) 716 (96%) 29 (4%) 2 (0%) 43 75

2 D 747/814 (92%) 716 (96%) 29 (4%) 2 (0%) 43 75

All All 2700/2936 (92%) 2444 (90%) 216 (8%) 40 (2%) 16 37

All (40) Ramachandran outliers are listed below:

Mol Chain Res Type1 A 6 LEU1 A 7 PRO1 A 112 LYS1 A 183 ILE1 A 263 ALA1 A 351 PRO1 A 592 VAL1 A 596 THR1 C 6 LEU1 C 7 PRO1 C 112 LYS1 C 183 ILE1 C 263 ALA1 C 351 PRO1 C 592 VAL1 C 596 THR1 A 22 GLU1 A 226 THR1 A 588 ILE2 B 679 ILE1 C 22 GLU1 C 226 THR1 C 588 ILE2 D 679 ILE1 A 18 LEU1 C 18 LEU1 A 79 VAL1 C 79 VAL1 A 224 TYR1 A 354 ASN2 B 342 ALA1 C 224 TYR1 C 354 ASN2 D 342 ALA



Continued from previous page...Mol Chain Res Type1 A 597 ILE1 C 597 ILE1 A 225 ILE1 C 225 ILE1 A 355 VAL1 C 355 VAL

5.3.2 Protein sidechains i○

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 527/572 (92%) 499 (95%) 28 (5%) 25 58

1 C 527/572 (92%) 499 (95%) 28 (5%) 25 58

2 B 662/720 (92%) 658 (99%) 4 (1%) 87 96

2 D 662/720 (92%) 658 (99%) 4 (1%) 87 96

All All 2378/2584 (92%) 2314 (97%) 64 (3%) 51 80

All (64) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 8 ASN1 A 14 ARG1 A 18 LEU1 A 20 GLU1 A 26 GLN1 A 57 ARG1 A 75 LEU1 A 78 LEU1 A 80 LEU1 A 85 LEU1 A 114 LEU1 A 120 LEU1 A 129 TYR1 A 206 SER1 A 229 LEU


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_sidechains


Continued from previous page...Mol Chain Res Type1 A 234 LEU1 A 237 PHE1 A 261 GLU1 A 354 ASN1 A 356 THR1 A 436 MET1 A 443 LEU1 A 461 LEU1 A 464 LEU1 A 588 ILE1 A 595 LEU1 A 604 LYS1 A 605 LEU2 B 133 CYS2 B 344 CYS2 B 680 SER2 B 761 ILE1 C 8 ASN1 C 14 ARG1 C 18 LEU1 C 20 GLU1 C 26 GLN1 C 57 ARG1 C 75 LEU1 C 78 LEU1 C 80 LEU1 C 85 LEU1 C 114 LEU1 C 120 LEU1 C 129 TYR1 C 206 SER1 C 229 LEU1 C 234 LEU1 C 237 PHE1 C 261 GLU1 C 354 ASN1 C 356 THR1 C 436 MET1 C 443 LEU1 C 461 LEU1 C 464 LEU1 C 588 ILE



Continued from previous page...Mol Chain Res Type1 C 595 LEU1 C 604 LYS1 C 605 LEU2 D 133 CYS2 D 344 CYS2 D 680 SER2 D 761 ILE

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (29) suchsidechains are listed below:

Mol Chain Res Type1 A 159 GLN1 A 293 ASN1 A 297 ASN2 B 33 ASN2 B 42 GLN2 B 64 ASN2 B 98 GLN2 B 101 GLN2 B 194 ASN2 B 373 HIS2 B 505 HIS2 B 586 ASN2 B 599 ASN2 B 718 ASN1 C 159 GLN1 C 293 ASN1 C 297 ASN2 D 33 ASN2 D 42 GLN2 D 64 ASN2 D 98 GLN2 D 101 GLN2 D 117 ASN2 D 194 ASN2 D 373 HIS2 D 505 HIS2 D 586 ASN2 D 599 ASN2 D 718 ASN


5.3.3 RNA i○

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains i○

There are no non-standard protein/DNA/RNA residues in this entry.

5.5 Carbohydrates i○

There are no carbohydrates in this entry.

5.6 Ligand geometry i○

Of 44 ligands modelled in this entry, 2 are monoatomic - leaving 42 for Mogul analysis.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

3 NAG A 701 1 14,14,15 0.53 0 17,19,21 0.45 03 NAG A 702 1 14,14,15 0.36 0 17,19,21 0.38 03 NAG A 703 1,3 14,14,15 0.82 1 (7%) 17,19,21 1.04 2 (11%)3 NAG A 704 3 14,14,15 0.51 0 17,19,21 0.37 03 NAG A 705 1 14,14,15 0.42 0 17,19,21 0.45 03 NAG A 706 1 14,14,15 0.42 0 17,19,21 0.73 1 (5%)4 3PH A 707 - 47,47,47 0.96 2 (4%) 51,52,52 1.11 3 (5%)4 3PH A 708 - 47,47,47 0.91 2 (4%) 51,52,52 1.13 3 (5%)3 NAG B 901 3,2 14,14,15 0.31 0 17,19,21 0.67 1 (5%)3 NAG B 902 3 14,14,15 0.24 0 17,19,21 0.57 03 NAG B 903 3,2 14,14,15 0.30 0 17,19,21 0.62 1 (5%)3 NAG B 904 3 14,14,15 0.27 0 17,19,21 0.51 03 NAG B 905 3,2 14,14,15 0.65 0 17,19,21 1.01 1 (5%)3 NAG B 906 3 14,14,15 0.22 0 17,19,21 0.64 1 (5%)3 NAG B 907 2 14,14,15 0.38 0 17,19,21 0.61 1 (5%)

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#rna

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligands




Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

3 NAG B 908 3,2 14,14,15 0.38 0 17,19,21 0.56 03 NAG B 909 3 14,14,15 0.28 0 17,19,21 0.46 03 NAG B 910 3,2 14,14,15 0.24 0 17,19,21 0.56 03 NAG B 911 3 14,14,15 0.34 0 17,19,21 0.42 03 NAG B 912 3,2 14,14,15 0.31 0 17,19,21 0.60 03 NAG B 913 3 14,14,15 0.22 0 17,19,21 0.67 1 (5%)3 NAG C 701 1 14,14,15 0.53 0 17,19,21 0.45 03 NAG C 702 1 14,14,15 0.36 0 17,19,21 0.38 03 NAG C 703 1,3 14,14,15 0.82 1 (7%) 17,19,21 1.04 2 (11%)3 NAG C 704 3 14,14,15 0.51 0 17,19,21 0.37 03 NAG C 705 1 14,14,15 0.42 0 17,19,21 0.45 03 NAG C 706 1 14,14,15 0.42 0 17,19,21 0.73 1 (5%)4 3PH C 707 - 47,47,47 0.96 2 (4%) 51,52,52 1.11 3 (5%)4 3PH C 708 - 47,47,47 0.91 2 (4%) 51,52,52 1.13 3 (5%)3 NAG D 901 3,2 14,14,15 0.31 0 17,19,21 0.67 1 (5%)3 NAG D 902 3 14,14,15 0.24 0 17,19,21 0.57 03 NAG D 903 3,2 14,14,15 0.30 0 17,19,21 0.62 1 (5%)3 NAG D 904 3 14,14,15 0.27 0 17,19,21 0.51 03 NAG D 905 3,2 14,14,15 0.65 0 17,19,21 1.01 1 (5%)3 NAG D 906 3 14,14,15 0.22 0 17,19,21 0.64 1 (5%)3 NAG D 907 2 14,14,15 0.38 0 17,19,21 0.61 1 (5%)3 NAG D 908 3,2 14,14,15 0.38 0 17,19,21 0.56 03 NAG D 909 3 14,14,15 0.28 0 17,19,21 0.46 03 NAG D 910 3,2 14,14,15 0.24 0 17,19,21 0.56 03 NAG D 911 3 14,14,15 0.34 0 17,19,21 0.42 03 NAG D 912 3,2 14,14,15 0.31 0 17,19,21 0.60 03 NAG D 913 3 14,14,15 0.22 0 17,19,21 0.67 1 (5%)

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.

Mol Type Chain Res Link Chirals Torsions Rings3 NAG A 701 1 - 2/6/23/26 0/1/1/13 NAG A 702 1 - 0/6/23/26 0/1/1/13 NAG A 703 1,3 - 2/6/23/26 0/1/1/13 NAG A 704 3 - 2/6/23/26 0/1/1/13 NAG A 705 1 - 2/6/23/26 0/1/1/1



Continued from previous page...Mol Type Chain Res Link Chirals Torsions Rings3 NAG A 706 1 - 0/6/23/26 0/1/1/14 3PH A 707 - - 18/49/49/49 -4 3PH A 708 - - 21/49/49/49 -3 NAG B 901 3,2 - 1/6/23/26 0/1/1/13 NAG B 902 3 - 0/6/23/26 0/1/1/13 NAG B 903 3,2 - 0/6/23/26 0/1/1/13 NAG B 904 3 - 2/6/23/26 0/1/1/13 NAG B 905 3,2 - 2/6/23/26 0/1/1/13 NAG B 906 3 - 1/6/23/26 0/1/1/13 NAG B 907 2 - 0/6/23/26 0/1/1/13 NAG B 908 3,2 - 1/6/23/26 0/1/1/13 NAG B 909 3 - 2/6/23/26 0/1/1/13 NAG B 910 3,2 - 2/6/23/26 0/1/1/13 NAG B 911 3 - 2/6/23/26 0/1/1/13 NAG B 912 3,2 - 2/6/23/26 0/1/1/13 NAG B 913 3 - 2/6/23/26 0/1/1/13 NAG C 701 1 - 2/6/23/26 0/1/1/13 NAG C 702 1 - 0/6/23/26 0/1/1/13 NAG C 703 1,3 - 2/6/23/26 0/1/1/13 NAG C 704 3 - 2/6/23/26 0/1/1/13 NAG C 705 1 - 2/6/23/26 0/1/1/13 NAG C 706 1 - 0/6/23/26 0/1/1/14 3PH C 707 - - 18/49/49/49 -4 3PH C 708 - - 21/49/49/49 -3 NAG D 901 3,2 - 1/6/23/26 0/1/1/13 NAG D 902 3 - 0/6/23/26 0/1/1/13 NAG D 903 3,2 - 0/6/23/26 0/1/1/13 NAG D 904 3 - 2/6/23/26 0/1/1/13 NAG D 905 3,2 - 2/6/23/26 0/1/1/13 NAG D 906 3 - 1/6/23/26 0/1/1/13 NAG D 907 2 - 0/6/23/26 0/1/1/13 NAG D 908 3,2 - 1/6/23/26 0/1/1/13 NAG D 909 3 - 2/6/23/26 0/1/1/13 NAG D 910 3,2 - 2/6/23/26 0/1/1/13 NAG D 911 3 - 2/6/23/26 0/1/1/13 NAG D 912 3,2 - 2/6/23/26 0/1/1/13 NAG D 913 3 - 2/6/23/26 0/1/1/1


All (10) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)4 A 707 3PH O31-C31 4.34 1.46 1.334 C 707 3PH O31-C31 4.34 1.46 1.334 A 707 3PH O21-C21 4.06 1.45 1.344 C 707 3PH O21-C21 4.06 1.45 1.344 A 708 3PH O21-C21 3.98 1.45 1.344 C 708 3PH O21-C21 3.98 1.45 1.344 A 708 3PH O31-C31 3.95 1.45 1.334 C 708 3PH O31-C31 3.95 1.45 1.333 C 703 NAG O5-C1 -2.86 1.39 1.433 A 703 NAG O5-C1 -2.86 1.39 1.43

All (30) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)4 A 708 3PH O21-C21-C22 4.34 120.98 111.514 C 708 3PH O21-C21-C22 4.34 120.98 111.514 A 707 3PH O21-C21-C22 3.93 120.09 111.514 C 707 3PH O21-C21-C22 3.93 120.09 111.514 A 707 3PH O31-C31-C32 3.10 121.89 111.934 C 707 3PH O31-C31-C32 3.10 121.89 111.933 D 905 NAG C1-O5-C5 3.06 116.36 112.203 B 905 NAG C1-O5-C5 3.06 116.36 112.203 C 706 NAG C1-O5-C5 2.68 115.85 112.203 A 706 NAG C1-O5-C5 2.68 115.85 112.204 A 708 3PH O31-C31-C32 2.66 120.48 111.934 C 708 3PH O31-C31-C32 2.66 120.48 111.934 A 708 3PH C2-O21-C21 -2.49 111.60 117.824 C 708 3PH C2-O21-C21 -2.49 111.60 117.823 B 913 NAG C1-O5-C5 2.35 115.39 112.203 D 913 NAG C1-O5-C5 2.35 115.39 112.203 D 906 NAG C1-O5-C5 2.26 115.28 112.203 B 906 NAG C1-O5-C5 2.26 115.28 112.203 C 703 NAG O4-C4-C5 -2.21 103.77 109.293 A 703 NAG O4-C4-C5 -2.21 103.77 109.293 B 907 NAG C1-O5-C5 2.13 115.10 112.203 D 907 NAG C1-O5-C5 2.13 115.10 112.204 A 707 3PH C2-O21-C21 -2.05 112.69 117.824 C 707 3PH C2-O21-C21 -2.05 112.69 117.823 C 703 NAG C4-C3-C2 2.04 114.01 111.023 A 703 NAG C4-C3-C2 2.04 114.01 111.023 D 903 NAG C1-O5-C5 2.03 114.96 112.203 B 903 NAG C1-O5-C5 2.03 114.96 112.20



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 D 901 NAG C1-O5-C5 2.03 114.96 112.203 B 901 NAG C1-O5-C5 2.03 114.96 112.20

There are no chirality outliers.

All (128) torsion outliers are listed below:

Mol Chain Res Type Atoms4 A 708 3PH C1-O11-P-O134 A 708 3PH C1-O11-P-O144 C 708 3PH C1-O11-P-O134 C 708 3PH C1-O11-P-O144 A 707 3PH C1-O11-P-O134 A 707 3PH C1-O11-P-O124 C 707 3PH C1-O11-P-O134 C 707 3PH C1-O11-P-O123 D 911 NAG O5-C5-C6-O63 B 913 NAG O5-C5-C6-O63 B 911 NAG O5-C5-C6-O63 D 913 NAG O5-C5-C6-O63 B 910 NAG O5-C5-C6-O63 D 910 NAG O5-C5-C6-O63 B 904 NAG O5-C5-C6-O63 D 904 NAG O5-C5-C6-O63 C 703 NAG C4-C5-C6-O63 A 703 NAG C4-C5-C6-O63 D 911 NAG C4-C5-C6-O63 B 913 NAG C4-C5-C6-O63 B 911 NAG C4-C5-C6-O63 D 913 NAG C4-C5-C6-O63 D 905 NAG C4-C5-C6-O63 B 909 NAG C4-C5-C6-O63 B 905 NAG C4-C5-C6-O63 D 909 NAG C4-C5-C6-O63 C 703 NAG O5-C5-C6-O63 A 703 NAG O5-C5-C6-O63 D 905 NAG O5-C5-C6-O63 B 905 NAG O5-C5-C6-O63 C 704 NAG C4-C5-C6-O63 A 704 NAG C4-C5-C6-O63 B 904 NAG C4-C5-C6-O63 D 904 NAG C4-C5-C6-O64 A 707 3PH C32-C31-O31-C3



Continued from previous page...Mol Chain Res Type Atoms4 C 707 3PH C32-C31-O31-C33 B 910 NAG C4-C5-C6-O63 D 910 NAG C4-C5-C6-O63 C 705 NAG O5-C5-C6-O63 A 705 NAG O5-C5-C6-O63 C 704 NAG O5-C5-C6-O63 A 704 NAG O5-C5-C6-O64 A 707 3PH O32-C31-O31-C34 C 707 3PH O32-C31-O31-C33 A 701 NAG O5-C5-C6-O63 C 701 NAG O5-C5-C6-O63 C 705 NAG C4-C5-C6-O63 A 705 NAG C4-C5-C6-O63 B 909 NAG O5-C5-C6-O63 D 909 NAG O5-C5-C6-O64 A 707 3PH C35-C36-C37-C384 C 707 3PH C35-C36-C37-C383 B 912 NAG C4-C5-C6-O63 D 912 NAG C4-C5-C6-O64 A 707 3PH C26-C27-C28-C294 A 707 3PH C3D-C3E-C3F-C3G4 C 707 3PH C26-C27-C28-C294 C 707 3PH C3D-C3E-C3F-C3G4 A 708 3PH C22-C21-O21-C24 C 708 3PH C22-C21-O21-C24 A 708 3PH C21-C22-C23-C244 C 708 3PH C21-C22-C23-C244 A 708 3PH C36-C37-C38-C394 C 708 3PH C36-C37-C38-C394 A 708 3PH C31-C32-C33-C344 C 708 3PH C31-C32-C33-C344 A 708 3PH C28-C29-C2A-C2B4 C 708 3PH C28-C29-C2A-C2B4 A 708 3PH O22-C21-O21-C24 C 708 3PH O22-C21-O21-C24 A 707 3PH O21-C2-C3-O314 C 707 3PH O21-C2-C3-O314 A 708 3PH C2E-C2F-C2G-C2H4 C 708 3PH C2E-C2F-C2G-C2H4 A 707 3PH C3E-C3F-C3G-C3H4 C 707 3PH C3E-C3F-C3G-C3H4 A 708 3PH C1-O11-P-O12



Continued from previous page...Mol Chain Res Type Atoms4 C 708 3PH C1-O11-P-O124 A 707 3PH C24-C25-C26-C274 C 707 3PH C24-C25-C26-C273 B 912 NAG O5-C5-C6-O63 D 912 NAG O5-C5-C6-O64 A 707 3PH C25-C26-C27-C284 C 707 3PH C25-C26-C27-C284 A 707 3PH C3B-C3C-C3D-C3E4 C 707 3PH C3B-C3C-C3D-C3E4 A 707 3PH C1-C2-C3-O314 C 707 3PH C1-C2-C3-O313 A 701 NAG C4-C5-C6-O63 C 701 NAG C4-C5-C6-O64 A 708 3PH C3B-C3C-C3D-C3E4 C 708 3PH C3B-C3C-C3D-C3E3 D 901 NAG C4-C5-C6-O63 B 901 NAG C4-C5-C6-O64 A 708 3PH C3D-C3E-C3F-C3G4 C 708 3PH C3D-C3E-C3F-C3G4 A 708 3PH O11-C1-C2-C34 C 708 3PH O11-C1-C2-C34 A 707 3PH C32-C33-C34-C354 C 707 3PH C32-C33-C34-C354 A 708 3PH O11-C1-C2-O214 C 708 3PH O11-C1-C2-O214 A 708 3PH O21-C2-C3-O314 C 708 3PH O21-C2-C3-O314 A 707 3PH C22-C23-C24-C254 C 707 3PH C22-C23-C24-C254 A 708 3PH C33-C34-C35-C364 C 708 3PH C33-C34-C35-C364 A 708 3PH C1-C2-C3-O314 C 708 3PH C1-C2-C3-O314 A 707 3PH C31-C32-C33-C344 C 707 3PH C31-C32-C33-C344 A 708 3PH C29-C2A-C2B-C2C4 C 708 3PH C29-C2A-C2B-C2C4 A 708 3PH C32-C33-C34-C354 C 708 3PH C32-C33-C34-C354 A 707 3PH C1-O11-P-O144 C 707 3PH C1-O11-P-O144 A 707 3PH C3F-C3G-C3H-C3I



Continued from previous page...Mol Chain Res Type Atoms4 C 707 3PH C3F-C3G-C3H-C3I3 D 908 NAG C4-C5-C6-O63 B 908 NAG C4-C5-C6-O64 A 708 3PH C25-C26-C27-C284 C 708 3PH C25-C26-C27-C284 A 708 3PH C34-C35-C36-C374 C 708 3PH C34-C35-C36-C373 D 906 NAG C4-C5-C6-O63 B 906 NAG C4-C5-C6-O6

There are no ring outliers.

1 monomer is involved in 1 short contact:

Mol Chain Res Type Clashes Symm-Clashes4 A 708 3PH 1 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identified by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identified rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not find sufficientequivalents in the CSD to analyse the geometry.

Ligand 3PH A 707

Bond lengths Bond angles

Torsions Rings


Ligand 3PH A 708


Torsions Rings

Ligand 3PH C 707


Torsions Rings

Ligand 3PH C 708


Torsions Rings

5.7 Other polymers i○

There are no such residues in this entry.



5.8 Polymer linkage issues i○

There are no chain breaks in this entry.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#polymer_linkage

full wwpdb em model validation report i · 2020-03-03 · page3 fullwwpdbemmodelvalidationreport...

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