Research workbench

HLA-A24 in complex with HIV-1 NEF134-10(2F)

Analyse HLA-A24 in complex with HIV-1 NEF134-10(2F) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VXO
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, a-24 alpha chain; Beta-2-microglobulin; 10-mer…
UniProt: P05534, P61769, Q9YYU3
Pockets: 10 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% 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	99	0% helix, 49% strand	P61769
C, F	10-mer peptide from protein nef	protein	10	0% helix, 0% strand	Q9YYU3

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	709	0.71	0.78	60	empty
2	675	0.69	0.77	61	empty
3	787	0.67	0.75	78	empty
4	79	0.52	0.85	24	empty
5	67	0.45	0.82	16	empty

Interfaces

7 interfaces between chains.

A–B · 1324 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1323 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 940 Å² buried · 18 hydrogen bonds · protein-protein
D–F · 933 Å² buried · 19 hydrogen bonds · protein-protein
A–E · 346 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3VXO · HLA-A24 in complex with HIV-1 Nef134-10(2F) · 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 E 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 Q9YYU3
Elsewhere: RCSB PDB 3VXO · PDBe 3VXO · UniProt P05534 · UniProt P61769 · UniProt Q9YYU3

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