MolNFT v1 · #82533 · protein

Fragments bound to HIV-1 integrase

3VQ4 · Pol polyprotein: “Fragments bound to HIV-1 integrase”. X-ray diffraction, 3 ligands (0NX, CD, SO4), 5 pockets (best druggability 0.53). MolNFT v1 #82533 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VQ4
Type: protein
Length: 284 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pol polyprotein
UniProt: Q72498
Ligands: 0NX, CD, SO4
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pol polyprotein	protein	144	47% helix, 24% strand	Q72498
B	Pol polyprotein	protein	140	49% helix, 22% strand	Q72498

Ligands and binding sites

0NX · (5-phenyl-1,2-oxazol-3-yl)methanol · ligand · 3 copies · chains A, B
CD · Cadmium ion · metal · 4 copies · chains A, B
SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	145	0.53	0.80	23	0NX
2	144	0.49	0.78	19	empty
3	68	0.49	0.84	18	0NX
4	114	0.45	0.78	17	0NX
5	109	0.44	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 1497 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

3VQ4 · Fragments bound to HIV-1 integrase · the same entry in another collection · chain A against A, TM-score 1.00

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 Q72498
Elsewhere: RCSB PDB 3VQ4 · PDBe 3VQ4 · UniProt Q72498

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