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Crystal structure of protease inhibitor, KB62 in complex with wild type HIV-1 protease

Analyse Crystal structure of protease inhibitor, KB62 in complex with wild type HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GI5
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
UniProt: O38732
Ligands: K62, PO4
Pockets: 1 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease	protein	99	4% helix, 54% strand	O38732

Ligands and binding sites

K62 · (5S)-3-(3-Acetylphenyl)-N-[(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)pr opyl]-2-oxo-5-oxazolidinecarboxamide · ligand · chains A, B
PO4 · Phosphate ion · ion · 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	414	0.70	0.82	42	K62

Interfaces

1 interface between chains.

A–B · 1839 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

3GI5 · Crystal structure of protease inhibitor, KB62 in complex with wild type HIV-1 protease · 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 O38732
Elsewhere: RCSB PDB 3GI5 · PDBe 3GI5 · UniProt O38732

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