Research workbench

HLA-B*57:01 presenting the peptide aslnlpavsw

Analyse HLA-B*57:01 presenting the peptide aslnlpavsw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6V2O
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; Peptide ala-ser-leu-asn-leu-pro-ala-val-ser-TRP
UniProt: U6BR87, P61769
Pockets: 6 · best druggability 0.68

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	27% helix, 39% strand	U6BR87
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Peptide ala-ser-leu-asn-leu-pro-ala-val-ser-TRP	protein	10	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

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	615	0.68	0.77	54	empty
2	74	0.67	0.93	23	empty
3	193	0.53	0.78	33	empty
4	105	0.46	0.79	22	ACT
5	58	0.36	0.79	16	empty

Interfaces

2 interfaces between chains.

A–B · 1358 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 776 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6V2O · HLA-B*57:01 presenting the peptide ASLNLPAVSW · 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 U6BR87
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6V2O · PDBe 6V2O · UniProt U6BR87 · UniProt P61769

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