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Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with non-peptidic inhibitor, GRL008

Analyse Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NJS
Type: protein
Length: 396 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
UniProt: Q9J006
Ligands: G08
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protease	protein	99	7% helix, 57% strand	Q9J006

Ligands and binding sites

G08 · (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-carbamoylphenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate · ligand · 2 copies · chains A, B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	408	0.72	0.83	39	G08
2	411	0.72	0.83	46	G08

Interfaces

3 interfaces between chains.

C–D · 1891 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1888 Å² buried · 32 hydrogen bonds · protein-protein
A–D · 14 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4NJS · Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q9J006
Elsewhere: RCSB PDB 4NJS · PDBe 4NJS · UniProt Q9J006

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