Research workbench

T cell receptor-P53-HLA-A2 complex

Analyse T cell receptor-P53-HLA-A2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VRM
Type: protein
Length: 809 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; T-cell receptor 12-6, alfa chain; TCR 12-6…
UniProt: Q861F7, P61769, P04637
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	273	26% helix, 39% strand	Q861F7
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
D	T-cell receptor 12-6, alfa chain	protein	183	2% helix, 44% strand	—
E	TCR 12-6, beta chain	protein	244	7% helix, 48% strand	—
P	Cellular tumor antigen P53 peptide	protein	9	0% helix, 0% strand	P04637

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1031	0.72	0.76	84	empty
2	542	0.66	0.77	51	empty
3	94	0.51	0.83	22	empty
4	170	0.48	0.77	30	empty
5	120	0.40	0.76	21	empty

Interfaces

7 interfaces between chains.

D–E · 2076 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1325 Å² buried · 15 hydrogen bonds · protein-protein
A–P · 916 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 408 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 290 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

6VRM · T cell receptor-p53-HLA-A2 complex · the same entry in another collection · chain A against A, 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 Q861F7
Every structure of UniProt P61769
Every structure of UniProt P04637
Elsewhere: RCSB PDB 6VRM · PDBe 6VRM · UniProt Q861F7 · UniProt P61769 · UniProt P04637

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.