MolNFT v1 · #39104 · protein

Crystal structure of HLA-B5703 and HIV-1 peptide

2HJK · HLA class I histocompatibility antigen B-57: “Crystal structure of HLA-B5703 and HIV-1 peptide”. X-ray diffraction, 6 pockets (best druggability 0.70). MolNFT v1 #39104 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2HJK
Type: protein
Length: 384 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen B-57; Beta-2-microglobulin; Gag protein
UniProt: Q9MYI6, P61769, Q1M075
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen B-57	protein	274	28% helix, 39% strand	Q9MYI6
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Gag protein	protein	11	0% helix, 0% strand	Q1M075

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	630	0.70	0.78	54	empty
2	81	0.44	0.81	21	empty
3	109	0.44	0.78	21	empty
4	84	0.38	0.77	19	empty
5	58	0.35	0.78	15	empty

Interfaces

2 interfaces between chains.

A–B · 1274 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 879 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

2HJK · Crystal Structure of HLA-B5703 and HIV-1 peptide · 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 Q9MYI6
Every structure of UniProt P61769
Every structure of UniProt Q1M075
Elsewhere: RCSB PDB 2HJK · PDBe 2HJK · UniProt Q9MYI6 · UniProt P61769 · UniProt Q1M075

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