New crystal form of HIV-1 PROTEASE/SAQUINAVIR structure reveals carbamylation of N-terminal proline

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).

Ligands and binding sites

• ARF · Formamide · ligand · 2 copies · chains A, B
• ROC · (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide · ligand · 2 copies · chains A, B, C, D
• CL · Chloride ion · ion · chains B
• DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• C–D · 1865 Ų buried · 32 hydrogen bonds · protein-protein
• A–B · 1840 Ų buried · 32 hydrogen bonds · protein-protein
• B–D · 299 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 156 Ų buried · 0 hydrogen bonds · protein-protein
• B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 3K4V · New crystal form of HIV-1 Protease/Saquinavir structure reveals carbamylation of… · the same entry in another collection · chain B against B, 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 P03366
• Elsewhere: RCSB PDB 3K4V · PDBe 3K4V · UniProt P03366