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Crystal structure of HIV-1 protease (Q7K) in complex with lopinavir

Analyse Crystal structure of HIV-1 protease (Q7K) in complex with lopinavir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O4S
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
UniProt: P03367
Ligands: AB1, CL
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	Protease	protein	99	4% helix, 55% strand	P03367

Ligands and binding sites

AB1 · N-{1-benzyl-4-[2-(2,6-dimethyl-phenoxy)-acetylamino]-3-hydroxy-5-phenyl-pentyl}-3-methyl-2-(2-oxo-tetrahydro-pyrimidin-1-yl)-butyramide · ligand · chains A, B
CL · Chloride ion · ion · 4 copies · 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	407	0.74	0.84	45	AB1

Interfaces

1 interface between chains.

A–B · 1845 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

2O4S · Crystal Structure of HIV-1 Protease (Q7K) in Complex with Lopinavir · 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 P03367
Elsewhere: RCSB PDB 2O4S · PDBe 2O4S · UniProt P03367

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