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Proteins are built from amino-Proteins are built from amino-acids.acids.

Introduction

H |NH2-c-CO2H | R

Schema of a peptide bondSchema of a peptide bond

Peptide bonds are rigid and planar

NH2CH

R1

C

O

N

H

CHC

O

NCH

R2

R3

HOOC

N-terminus C-terminusPeptide bonds

THE MAIN STRUCTURE THE MAIN STRUCTURE DATABASESDATABASES

PDB: The repository for all known structural proteins.

SCOP: Structural Classification of Proteins

CATH: Class(C), Architecture(A), Topology(T) and Homologous superfamily (H). 

PDB

HEADER PLANT SEED PROTEIN 30-APR-81 1CRN 1CRND 1

COMPND CRAMBIN 1CRN 4

Seqres: Sequence of protein. Be aware: Not always all 3D coordinates are present for all the aminoacids in SEQRES

SEQRES 1 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE 1CRN 51SEQRES 2 46 ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA ILE CYS 1CRN 52SEQRES 3 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR 1CRN 53SEQRES 4 46 CYS PRO GLY ASP TYR ALA ASN 1CRN 54

Filename=accession number=PDB codeFilename is 4 positions (often 1 digit & 3 letters, i.e.: 1CRN)(if you see 1abcD, it means chain D of structure 1abc)

PDB RECORD (1)

Header: Describes molecule & gives deposition date

CMPND: Name of the molecule

ATOM 1 N THR 1 17.047 14.099 3.625 1.00 13.79 1CRN 70ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80 1CRN 71ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19 1CRN 72ATOM 4 O THR 1 15.268 13.825 5.594 1.00 9.85 1CRN 73ATOM 5 CB THR 1 18.170 12.703 5.337 1.00 13.02 1CRN 74ATOM 6 OG1 THR 1 19.334 12.829 4.463 1.00 15.06 1CRN 75ATOM 7 CG2 THR 1 18.150 11.546 6.304 1.00 14.23 1CRN 76ATOM 8 N THR 2 15.115 11.555 5.265 1.00 7.81 1CRN 77ATOM 9 CA THR 2 13.856 11.469 6.066 1.00 8.31 1CRN 78ATOM 10 C THR 2 14.164 10.785 7.379 1.00 5.80 1CRN 79ATOM 11 O THR 2 14.993 9.862 7.443 1.00 6.94 1CRN 80ATOM 12 CB THR 2 12.732 10.711 5.261 1.00 10.32 1CRN 81ATOM 13 OG1 THR 2 13.308 9.439 4.926 1.00 12.81 1CRN 82ATOM 14 CG2 THR 2 12.484 11.442 3.895 1.00 11.90 1CRN 83ATOM 15 N CYS 3 13.488 11.241 8.417 1.00 5.24 1CRN 84ATOM 16 CA CYS 3 13.660 10.707 9.787 1.00 5.39 1CRN 85

...

ATOM 324 CG ASN 46 12.538 4.304 14.922 1.00 7.98 1CRN 393ATOM 325 OD1 ASN 46 11.982 4.849 15.886 1.00 11.00 1CRN 394ATOM 326 ND2 ASN 46 13.407 3.298 15.015 1.00 10.32 1CRN 395ATOM 327 OXT ASN 46 12.703 4.973 10.746 1.00 7.86 1CRN 396TER 328 ASN 46 1CRN 397

ATOM: one line for each atom with its unique name and its, x, y, z, coordinates

PDB RECORD (2)

FOLD: Major structural similarity. Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangementand with the same topological connections

SUPERFAMILY: Probable common evolutionary origin. Proteins that have low sequences identities, but whose structural and functional features suggest that a common evolutionary origin is probable.

FAMILY: Clear evolutionary relationship. Proteins clustered together into families are clearly evolutionarily related. Generally, this means that pairwiseresidue identities between the proteins are 30% greater.

SCOP (Murzin, Brenner, Hubbard, Clothia, 1995)

•Classification according to visual analysis and comparison.

STRUCTURAL CLASSIFICATION OF PROTEINS

Only crystal structures solved to resolution better than 3.0 angstroms are considered

CATH hierarchyCATH hierarchy

Class: Seconday structure and packing

Architecture: overall shape domain structure and orientation (no conenctivities between the secondary structures)

Topology (FOLD family): overall shape and connectivities.

Homologous superfamily : prots are thought to share common ancestorSimilarities by seq. alignment and then by structure comparison usingSSAP