ProteinStructuralDatabases

Proteins are built from amino-acids. Introduction H | NH2-c-CO2H | R

Schema of a peptide bond Peptide bonds are rigid and planar NH2 CH R1 C O N H CH C O N R2 R3 HOOC N-terminus C-terminus Peptide bonds

THE MAIN STRUCTURE DATABASES 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 amino acids in SEQRES SEQRES 1 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE 1CRN 51 SEQRES 2 46 ASN VAL CYS ARG LEU PRO GLY THR PRO GLU ALA ILE CYS 1CRN 52 SEQRES 3 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR 1CRN 53 SEQRES 4 46 CYS PRO GLY ASP TYR ALA ASN 1CRN 54 Filename=accession number=PDB code Filename 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 CRN 70 ATOM 2 CA THR CRN 71 ATOM 3 C THR CRN 72 ATOM 4 O THR CRN 73 ATOM 5 CB THR CRN 74 ATOM 6 OG1 THR CRN 75 ATOM 7 CG2 THR CRN 76 ATOM 8 N THR CRN 77 ATOM 9 CA THR CRN 78 ATOM 10 C THR CRN 79 ATOM 11 O THR CRN 80 ATOM 12 CB THR CRN 81 ATOM 13 OG1 THR CRN 82 ATOM 14 CG2 THR CRN 83 ATOM 15 N CYS CRN 84 ATOM 16 CA CYS CRN ATOM 324 CG ASN CRN 393 ATOM 325 OD1 ASN CRN 394 ATOM 326 ND2 ASN CRN 395 ATOM 327 OXT ASN CRN 396 TER 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 arrangement and 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 pairwise residue 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 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 ancestor Similarities by seq. alignment and then by structure comparison using SSAP