Research workbench

HLA-B*27:05 presenting an HIV-1 6MER peptide

Analyse HLA-B*27:05 presenting an HIV-1 6MER peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VQZ
Type: protein
Length: 760 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; 6-mer peptide
UniProt: O78189, P61769
Ligands: ARG
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	MHC class I antigen	protein	275	27% helix, 42% strand	O78189
B, D	Beta-2-microglobulin	protein	99	0% helix, 52% strand	P61769
G, F	6-mer peptide	protein	6	0% helix, 0% strand	—

Ligands and binding sites

ARG · Arginine · ligand · 2 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 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	1152	0.77	0.80	95	empty
2	754	0.75	0.80	69	empty
3	571	0.69	0.78	49	empty
4	187	0.64	0.84	29	ARG
5	176	0.63	0.84	29	ARG

Interfaces

7 interfaces between chains.

C–D · 1336 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1241 Å² buried · 20 hydrogen bonds · protein-protein
C–G · 677 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 668 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 399 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6VQZ · HLA-B*27:05 presenting an HIV-1 6mer peptide · the same entry in another collection · chain F against F, 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 0.99

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 O78189
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6VQZ · PDBe 6VQZ · UniProt O78189 · UniProt P61769

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