Research workbench

HLA*A2402 complexed with HIV NEF138 Y2F mutant 10MER epitope

Analyse HLA*A2402 complexed with HIV NEF138 Y2F mutant 10MER epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HGD
Type: protein
Length: 768 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; Protein…
UniProt: P05534, P61769, P18801
Pockets: 11 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-24 alpha chain	protein	274	28% helix, 39% strand	P05534
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Protein nef	protein	10	0% helix, 0% strand	P18801

Pockets

11 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	686	0.70	0.78	59	empty
2	671	0.70	0.78	60	empty
3	687	0.67	0.76	56	empty
4	100	0.59	0.86	26	empty
5	116	0.49	0.80	28	empty

Interfaces

7 interfaces between chains.

A–B · 1350 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 1336 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 922 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 919 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 405 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5HGD · HLA*A2402 complexed with HIV nef138 Y2F mutant 10mer epitope · the same entry in another collection · chain F against F, 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 5HGD · PDBe 5HGD · UniProt P05534 · UniProt P61769 · UniProt P18801

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