MolNFT v1 · #146488 · protein

HIV-1 protease with single mutation L76V in complex with lopinavir

6DJ2: “HIV-1 protease with single mutation L76V in complex with lopinavir”. X-ray diffraction, 3 ligands (AB1, NA, CL), 1 pocket (best druggability 0.71). MolNFT v1 #146488 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DJ2
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
UniProt: Q5RZ08
Ligands: AB1, NA, CL
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease	protein	99	4% helix, 56% strand	Q5RZ08

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
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 3 copies · chains A, 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	391	0.71	0.83	41	AB1

Interfaces

1 interface between chains.

A–B · 1856 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

6DJ2 · HIV-1 protease with single mutation L76V 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 Q5RZ08
Elsewhere: RCSB PDB 6DJ2 · PDBe 6DJ2 · UniProt Q5RZ08

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