2NMY

Crystal structure analysis of HIV-1 protease mutant V82A with a inhibitor saquinavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.149

Literature

Macromolecules
Sequence Display for 2NMY

Classification: Hydrolase / HYDROLASE INHIBITOR

Total Structure Weight: 22286.05

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEASE A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: Q7K, L33I, L63I, C67A, V82A, C95A
Gene Name(s): pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ROC
Query on ROC

A (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
RO 31-8959, (Synonym)
C38 H50 N6 O5
QWAXKHKRTORLEM-UGJKXSETSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000454
Query on PRD_000454
A Saquinavir Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.149
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 59.99 α = 90.00
b = 87.46 β = 90.00
c = 47.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-10-23
  • Released Date: 2007-03-13
  • Deposition author(s): Tie, Y., Kovalevsky, A.Y., Boross, P., Wang, Y.F., Ghosh, A.K., Tozser, J., Harrison, R.W., Weber, I.T.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • 2013-02-27
    Type: Other