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X-ray crystal structure of wild type HIV-1 protease in complex with grl-085

Analyse X-ray crystal structure of wild type HIV-1 protease in complex with grl-085 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5COO
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 protease
UniProt: G0X8E3
Ligands: 52Z
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 protease	protein	99	4% helix, 51% strand	G0X8E3

Ligands and binding sites

52Z · (3R,3aS,4S,7aS)-3-hydroxyhexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-3-hydroxy-1-(4-methoxyphenyl)-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	361	0.69	0.82	34	52Z
2	56	0.41	0.81	12	empty

Interfaces

1 interface between chains.

A–B · 1705 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

5COO · X-ray crystal structure of wild type HIV-1 protease in complex with GRL-085 · 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 G0X8E3
Elsewhere: RCSB PDB 5COO · PDBe 5COO · UniProt G0X8E3

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