Research workbench

Structure of HIV-1 protease in complex with inhibitor kni-1657

Analyse Structure of HIV-1 protease in complex with inhibitor kni-1657 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YOK
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
Ligands: 8Z0
Pockets: 1 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease	protein	99	4% helix, 55% strand	—

Ligands and binding sites

8Z0 · (4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3-yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide · ligand · chains A, B
GOL · Glycerol · additive · 2 copies · 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	389	0.74	0.84	39	8Z0

Interfaces

1 interface between chains.

A–B · 1866 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

5YOK · Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657 · 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 5YOK · PDBe 5YOK

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.