MolNFT v1 · #167647 · protein

Complex of HLA-A2, a class I MHC, with a P53 peptide

6VR5 · MHC class I antigen: “Complex of HLA-A2, a class I MHC, with a P53 peptide”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #167647 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VR5
Type: protein
Length: 765 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Cellular tumor antigen P53 peptide
UniProt: Q861F7, P61769, P04637
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 20% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	274	28% helix, 41% strand	Q861F7
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769
D	MHC class I antigen	protein	275	27% helix, 40% strand	Q861F7
E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
P, Q	Cellular tumor antigen P53 peptide	protein	9	0% helix, 0% strand	P04637

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	946	0.71	0.76	87	empty
2	573	0.67	0.77	54	empty
3	174	0.49	0.77	29	empty
4	169	0.48	0.77	26	empty
5	91	0.44	0.79	20	empty

Interfaces

5 interfaces between chains.

D–E · 1314 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1220 Å² buried · 20 hydrogen bonds · protein-protein
A–P · 938 Å² buried · 17 hydrogen bonds · protein-protein
D–Q · 897 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 378 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6VR5 · Complex of HLA-A2, a class I MHC, with a p53 peptide · the same entry in another collection · chain Q against Q, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q861F7
Every structure of UniProt P61769
Every structure of UniProt P04637
Elsewhere: RCSB PDB 6VR5 · PDBe 6VR5 · UniProt Q861F7 · UniProt P61769 · UniProt P04637

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