MolNFT v1 · #137695 · protein

HLA-B*58:01 presenting lsspvtksw

5VWH · HLA class I histocompatibility antigen, B-58 alpha chain: “HLA-B*58:01 presenting lsspvtksw”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #137695 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VWH
Type: protein
Length: 385 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-58 alpha chain; Beta-2-microglobulin; Nonamer…
UniProt: P10319, P61769
Pockets: 5 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-58 alpha chain	protein	276	26% helix, 39% strand	P10319
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Nonamer peptide: leu-ser-ser-pro-val-thr-lys-ser-TRP	protein	9	0% helix, 0% strand	—

Pockets

5 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	630	0.69	0.78	53	empty
2	81	0.44	0.80	19	empty
3	95	0.41	0.78	24	empty
4	62	0.36	0.78	15	empty
5	58	0.31	0.75	16	empty

Interfaces

2 interfaces between chains.

A–B · 1430 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 884 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5VWH · HLA-B*58:01 presenting LSSPVTKSW · 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 P10319
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5VWH · PDBe 5VWH · UniProt P10319 · UniProt P61769

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