Research workbench

HLA-B*57:03 presenting the peptide lsspvtksf

Analyse HLA-B*57:03 presenting the peptide lsspvtksf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V2Q
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA-B alpha chain (B*5703GB); Beta-2-microglobulin; Peptide…
UniProt: I3ZN84, P61769
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA-B alpha chain (B*5703GB)	protein	276	27% helix, 39% strand	I3ZN84
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Peptide leu-ser-ser-pro-val-thr-lys-ser-phe	protein	9	0% helix, 0% strand	—

Ligands and binding sites

ACT · Acetate ion · additive · chains A, B

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

Pockets

4 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	610	0.68	0.77	56	empty
2	131	0.45	0.77	29	empty
3	91	0.43	0.79	22	ACT
4	56	0.36	0.79	15	empty

Interfaces

2 interfaces between chains.

A–B · 1378 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 852 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6V2Q · HLA-B*57:03 presenting the peptide LSSPVTKSF · 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 I3ZN84
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6V2Q · PDBe 6V2Q · UniProt I3ZN84 · UniProt P61769

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