Research workbench

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

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

PDB: 3VRJ
Type: protein
Length: 384 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
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, B-57 alpha chain	protein	275	28% helix, 39% strand	P18465
B	Beta-2-microglobulin	protein	99	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

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	152	0.82	0.97	30	1KX
2	512	0.69	0.79	46	empty
3	100	0.46	0.80	20	empty
4	57	0.36	0.79	13	empty
5	50	0.34	0.79	15	empty

Interfaces

2 interfaces between chains.

A–B · 1366 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 850 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3VRJ · HLA-B*57:01-LTTKLTNTNI 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 3VRJ · PDBe 3VRJ · UniProt P18465 · UniProt P61769

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