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Crystal structures of a multidrug-resistant HIV-1 protease reveal an expanded active site cavity

Analyse Crystal structures of a multidrug-resistant HIV-1 protease reveal an expanded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RQ9
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
EC: 3.4.23.16
Ligands: DMQ
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease (EC 3.4.23.16)	protein	99	7% helix, 48% strand	—

Ligands and binding sites

DMQ · [4-R-(-4-alpha,5-alpha,6-beta,7-beta)]-hexahydro-5,6-bis(hydroxy)-1,3-bis([(3-amino)phenyl]methyl)-4,7-bis(phenylmethyl)-2H-1,3-diazepinone · ligand · 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	408	0.55	0.73	39	DMQ

Interfaces

1 interface between chains.

A–B · 1505 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

1RQ9 · Crystal structures of a Multidrug-Resistant HIV-1 Protease Reveal an Expanded Active Site… · 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 1RQ9 · PDBe 1RQ9

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