Research workbench

TCR peptide HLA-A2 complex

Analyse TCR peptide 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: 7N6E
Type: protein
Length: 1,636 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Spike protein S1; TRAV12-1 TCR-alpha; TRBV19…
UniProt: Q861F7, P61769, P0DTC2
Pockets: 18 · best druggability 0.80

Structure

x-ray diffraction · 7 distinct chains · 13% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	271	27% helix, 39% strand	Q861F7
B, E	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C, F	Spike protein S1	protein	9	0% helix, 0% strand	P0DTC2
D	MHC class I antigen	protein	274	26% helix, 40% strand	Q861F7
G	TRAV12-1 TCR-alpha	protein	198	4% helix, 45% strand	—
I	TRAV12-1 TCR-alpha	protein	199	4% helix, 45% strand	—
H, J	TRBV19 TCR beta	protein	239	6% helix, 49% strand	—

Pockets

18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1143	0.80	0.81	95	empty
2	963	0.71	0.76	87	empty
3	641	0.71	0.78	52	empty
4	679	0.69	0.77	55	empty
5	666	0.69	0.77	54	empty

Interfaces

18 interfaces between chains.

G–H · 2238 Å² buried · 24 hydrogen bonds · protein-protein
I–J · 2236 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1346 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 1315 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 906 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

7N6E · TCR peptide HLA-A2 complex · the same entry in another collection · chain J against J, 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 P0DTC2
Elsewhere: RCSB PDB 7N6E · PDBe 7N6E · UniProt Q861F7 · UniProt P61769 · UniProt P0DTC2

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