MolNFT v1 · #41068 · protein

AH3 recognition of mutant HLA-A2 W167A

2JCC · HLA class I histocompatibility antigen, a-2 alpha chain: “AH3 recognition of mutant HLA-A2 W167A”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #41068 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2JCC
Type: protein
Length: 1,630 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; P1049; TCR…
UniProt: P01892, P61769
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	P01892
B, I	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, J	P1049	protein	9	0% helix, 0% strand	—
E, L	TCR alpha	protein	194	3% helix, 41% strand	—
F, M	TCR beta	protein	237	7% helix, 52% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1192	0.76	0.78	98	empty
2	770	0.72	0.78	76	empty
3	626	0.71	0.79	55	empty
4	682	0.70	0.78	63	empty
5	164	0.54	0.80	29	empty

Interfaces

18 interfaces between chains.

E–F · 2289 Å² buried · 33 hydrogen bonds · protein-protein
L–M · 2266 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1461 Å² buried · 22 hydrogen bonds · protein-protein
H–I · 1361 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 860 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide (disulfide).

Compared structures

2JCC · AH3 recognition of mutant HLA-A2 W167A · the same entry in another collection · chain M against M, 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 P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 2JCC · PDBe 2JCC · UniProt P01892 · UniProt P61769

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