Research workbench

HLA*A2402 complex with HIV NEF138 Y2F-8MER mutant epitope

Analyse HLA*A2402 complex with HIV NEF138 Y2F-8MER mutant epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HGA
Type: protein
Length: 764 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-24 alpha chain; Beta-2-microglobulin; 8-mer…
UniProt: P05534, P61769, P18801
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-24 alpha chain	protein	274	27% helix, 40% strand	P05534
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	8-mer from protein nef	protein	8	0% helix, 0% strand	P18801

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	626	0.79	0.84	63	empty
2	710	0.71	0.78	57	empty
3	398	0.70	0.82	46	empty
4	227	0.55	0.78	34	empty
5	115	0.47	0.79	22	empty

Interfaces

8 interfaces between chains.

D–E · 1355 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1332 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 948 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 944 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 425 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5HGA · HLA*A2402 complex with HIV nef138 Y2F-8mer mutant epitope · the same entry in another collection · chain B against B, 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 P05534
Every structure of UniProt P61769
Every structure of UniProt P18801
Elsewhere: RCSB PDB 5HGA · PDBe 5HGA · UniProt P05534 · UniProt P61769 · UniProt P18801

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