MolNFT v1 · #82786 · protein

HLA-A24 in complex with HIV-1 NEF134-10(6L)

3VXP · HLA class I histocompatibility antigen, a-24 alpha chain: “HLA-A24 in complex with HIV-1 NEF134-10(6L)”. X-ray diffraction, 9 pockets (best druggability 0.72). MolNFT v1 #82786 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3VXP
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; 10-mer…
UniProt: P05534, P61769, Q9WPU2
Pockets: 9 · best druggability 0.72

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, 51% strand	P61769
C, F	10-mer peptide from protein nef	protein	10	0% helix, 0% strand	Q9WPU2

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	709	0.72	0.79	62	empty
2	615	0.69	0.77	54	empty
3	616	0.68	0.77	51	empty
4	137	0.46	0.77	22	empty
5	57	0.43	0.82	17	empty

Interfaces

6 interfaces between chains.

A–B · 1355 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1345 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 1010 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 999 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 285 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3VXP · HLA-A24 in complex with HIV-1 Nef134-10(6L) · 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 Q9WPU2
Elsewhere: RCSB PDB 3VXP · PDBe 3VXP · UniProt P05534 · UniProt P61769 · UniProt Q9WPU2

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