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: 6VRN
Type: protein
Length: 813 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 38-10, alfa chain; TCR…
UniProt: Q861F7, P61769, P04637
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 13% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	274	27% helix, 40% strand	Q861F7
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
D	T-cell receptor 38-10, alfa chain	protein	188	5% helix, 48% strand	—
E	TCR repeptor 38-10, beta chain	protein	242	7% helix, 52% strand	—
P	Cellular tumor antigen P53 peptide	protein	9	0% helix, 0% strand	P04637

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.70	0.75	76	empty
2	647	0.68	0.77	59	empty
3	304	0.59	0.78	35	empty
4	242	0.54	0.77	48	empty
5	122	0.52	0.81	22	empty

Interfaces

7 interfaces between chains.

D–E · 2269 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1283 Å² buried · 16 hydrogen bonds · protein-protein
A–P · 894 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 360 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 347 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6VRN · 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 6VRN · PDBe 6VRN · UniProt Q861F7 · UniProt P61769 · UniProt P04637

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