Research workbench

HLA-B*15:02 complexed with a synthetic peptide

Analyse HLA-B*15:02 complexed with a synthetic peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VB6
Type: protein
Length: 384 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Synthetic peptide…
UniProt: F4NBQ8, P61769
Pockets: 4 · 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	27% helix, 39% strand	F4NBQ8
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Synthetic peptide thr-val-arg-ala-ser-gly-his-ser-tyr	protein	9	0% helix, 0% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B
ACT · Acetate ion · additive · chains A, C

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

Pockets

4 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	638	0.69	0.78	55	GOL
2	159	0.50	0.78	26	GOL
3	123	0.48	0.79	18	empty
4	55	0.38	0.80	16	empty

Interfaces

2 interfaces between chains.

A–B · 1301 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 891 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6VB6 · HLA-B*15:02 complexed with a synthetic 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 F4NBQ8
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6VB6 · PDBe 6VB6 · UniProt F4NBQ8 · UniProt P61769

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