2NMY

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

Structural Biology Knowledgebase: 2NMY SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2NMY

Classification: Hydrolase / HYDROLASE INHIBITOR

Total Structure Weight: 22286.20

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

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

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

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ROC IC50: 0.2 - 270 nM (92) BindingDB
Kd: 0.31 - 0.315 nM (92) BindingDB
Ki: 0.062 - 117 nM (92) BindingDB

N/A in BindingMoad
Ki: 4.3 nM  PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000454 (NTB,ASN,HP0,QNC) 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
  • Electron Density Server: EDS EDS

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

  • 2013-02-27
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Atom occupancy | Details: Restore author's atom occupancy
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence