Research workbench

HLA-B*57:01 complexed to pep-V and abacavir

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

PDB: 3UPR
Type: protein
Length: 766 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, B-57 alpha chain; Pep-V; Beta-2-microglobulin
UniProt: P18465, P61769
Ligands: 1KX, CL
Pockets: 12 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	HLA class I histocompatibility antigen, B-57 alpha chain	protein	275	26% helix, 39% strand	P18465
P, Q	Pep-V	protein	9	0% helix, 0% strand	—
B, D	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Ligands and binding sites

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

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1014	0.82	0.83	101	empty
2	141	0.81	0.97	25	1KX
3	130	0.80	0.97	24	1KX
4	571	0.70	0.79	53	empty
5	452	0.68	0.80	43	empty

Interfaces

7 interfaces between chains.

A–B · 1413 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1397 Å² buried · 24 hydrogen bonds · protein-protein
Q–C · 785 Å² buried · 17 hydrogen bonds · protein-protein
A–P · 779 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 285 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3UPR · HLA-B*57:01 complexed to pep-V and Abacavir · the same entry in another collection · chain D against D, 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 P18465
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3UPR · PDBe 3UPR · UniProt P18465 · UniProt P61769

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