MolNFT v1 · #7993 · protein

HIV-1 protease mutant with val 82 replaced by asp (V82D) complexed with U89360E (inhibitor)

1GNM: “HIV-1 protease mutant with val 82 replaced by asp (V82D) complexed with U89360E (inhibitor)”. X-ray diffraction, 1 ligand (U0E), 1 pocket (best druggability 0.70). MolNFT v1 #7993 on GenesisL1: 3D structure, binding sites and…

PDB: 1GNM
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
EC: 2.7.7.49
UniProt: P03368
Ligands: U0E
Pockets: 1 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease (EC 2.7.7.49)	protein	99	4% helix, 55% strand	P03368

Ligands and binding sites

U0E · N-[[1-[N-acetamidyl]-[1-cyclohexylmethyl-2-hydroxy-4-isopropyl]-but-4-yl]-carbonyl]-glutaminyl-arginyl-amide · ligand · 2 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	348	0.70	0.83	35	U0E

Interfaces

1 interface between chains.

A–B · 1879 Å² buried · 37 hydrogen bonds · protein-protein

Compared structures

1GNM · HIV-1 protease mutant with val 82 replaced by asp (V82D) complexed with U89360E… · 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 P03368
Elsewhere: RCSB PDB 1GNM · PDBe 1GNM · UniProt P03368

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