MolNFT v1 · #89476 · protein

Crystal structure of wild-type HIV-1 protease in complex with drv

4DQB · Aspartyl protease: “Crystal structure of wild-type HIV-1 protease in complex with drv”. X-ray diffraction, 2 ligands (017, PO4), 1 pocket (best druggability 0.71). MolNFT v1 #89476 on GenesisL1: 3D structure, binding sites and…

PDB: 4DQB
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartyl protease
Ligands: 017, PO4
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aspartyl protease	protein	99	4% helix, 57% strand	—

Ligands and binding sites

017 · (3r,3as,6ar)-hexahydrofuro[2,3-b]furan-3-yl(1s,2r)-3-[[(4-aminophenyl)sulfonyl](isobutyl)amino]-1-benzyl-2-hydroxypropylcarbamate · ligand · chains A, B
PO4 · Phosphate ion · ion · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	351	0.71	0.83	35	017

Interfaces

1 interface between chains.

A–B · 1857 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

4DQB · Crystal Structure of wild-type HIV-1 Protease in Complex with DRV · 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
Elsewhere: RCSB PDB 4DQB · PDBe 4DQB

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