MolNFT v1 · #167630 · protein

T cell receptor-P53-HLA-A2 complex

6VQO · MHC class I antigen: “T cell receptor-P53-HLA-A2 complex”. X-ray diffraction, 20 pockets (best druggability 0.73). MolNFT v1 #167630 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VQO
Type: protein
Length: 1,614 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; T-cell receptor 1A2, alfa chain; TCR receptor…
UniProt: F6IQS2, P61769
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 9 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	273	26% helix, 39% strand	F6IQS2
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
D	T-cell receptor 1A2, alfa chain	protein	193	2% helix, 49% strand	—
E	TCR receptor 1A2, beta chain	protein	240	7% helix, 47% strand	—
F	MHC class I antigen	protein	254	26% helix, 35% strand	F6IQS2
G	Beta-2-microglobulin	protein	99	0% helix, 47% strand	P61769
H	T-cell receptor 1A2, alfa chain	protein	196	2% helix, 49% strand	—
J	TCR receptor 1A2, beta chain	protein	241	6% helix, 51% strand	—
P, Q	Peptide from P53 tumor suppressor	protein	9	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.73	0.76	76	empty
2	993	0.71	0.75	74	empty
3	486	0.67	0.78	47	empty
4	622	0.66	0.76	56	empty
5	290	0.55	0.76	45	empty

Interfaces

16 interfaces between chains.

H–J · 2136 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 2106 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1306 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 1183 Å² buried · 14 hydrogen bonds · protein-protein
A–P · 900 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

6VQO · T cell receptor-p53-HLA-A2 complex · 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 B against A, TM-score 0.98

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 F6IQS2
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6VQO · PDBe 6VQO · UniProt F6IQS2 · UniProt P61769

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