MolNFT v1 · #82580 · protein

HLA-B*57:01-rvaqlenvyi in complex with abacavir

3VRI · HLA class I histocompatibility antigen, B-57 alpha chain: “HLA-B*57:01-rvaqlenvyi in complex with abacavir”. X-ray diffraction, 2 ligands (1KX, SO4), 6 pockets (best druggability 0.80). MolNFT v1 #82580 on GenesisL1: 3D structure…

PDB: 3VRI
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-57 alpha chain; Beta-2-microglobulin; 10-mer…
UniProt: P18465, P61769
Ligands: 1KX, SO4
Pockets: 6 · best druggability 0.80

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-57 alpha chain	protein	275	27% helix, 39% strand	P18465
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	10-mer peptide	protein	10	0% helix, 0% strand	—

Ligands and binding sites

1KX · {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol · ligand · chains A, C
SO4 · Sulfate ion · ion · chains A

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

Pockets

6 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	189	0.80	0.94	31	1KX
2	563	0.68	0.78	55	empty
3	99	0.47	0.80	19	empty
4	70	0.37	0.78	14	empty
5	57	0.32	0.76	16	empty

Interfaces

2 interfaces between chains.

A–B · 1400 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 827 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3VRI · HLA-B*57:01-RVAQLENVYI in complex with abacavir · 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 0.99

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 P18465
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3VRI · PDBe 3VRI · UniProt P18465 · UniProt P61769

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.