MolNFT v1 · #137693 · protein

HLA-B*58:03 presenting ltvqvarvy

5VWF · MHC class I antigen: “HLA-B*58:03 presenting ltvqvarvy”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #137693 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VWF
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Nonamer 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	MHC class I antigen	protein	276	26% helix, 39% strand	I3ZN84
B	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P61769
C	Nonamer peptide: leu-thr-val-gln-val-ala-arg-val-tyr	protein	9	0% helix, 0% strand	—

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	650	0.68	0.77	62	empty
2	114	0.46	0.79	25	empty
3	130	0.46	0.77	23	empty
4	80	0.37	0.77	15	empty

Interfaces

2 interfaces between chains.

A–B · 1224 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 905 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5VWF · HLA-B*58:03 presenting LTVQVARVY · 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 5VWF · PDBe 5VWF · UniProt I3ZN84 · UniProt P61769

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