Research workbench

HLA-B*27:05 presenting an HIV-1 13MER peptide

Analyse HLA-B*27:05 presenting an HIV-1 13MER peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VQE
Type: protein
Length: 386 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; 13-mer peptide
UniProt: O78189, P61769
Pockets: 5 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	28% helix, 40% strand	O78189
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	13-mer peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	647	0.69	0.77	58	GOL
2	87	0.61	0.88	19	empty
3	108	0.46	0.79	18	empty
4	107	0.45	0.79	23	GOL
5	69	0.36	0.77	15	empty

Interfaces

2 interfaces between chains.

A–B · 1348 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1027 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6VQE · HLA-B*27:05 presenting an HIV-1 13mer 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 0.99

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 6VQE · PDBe 6VQE · UniProt O78189 · UniProt P61769

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