2FXD

X-ray crystal structure of HIV-1 protease IRM mutant complexed with atazanavir (BMS-232632)

Structural Biology Knowledgebase: 2FXD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.235

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FXD

Classification: HYDROLASE

Total Structure Weight: 22379.53

Macromolecule Entities
Molecule Chains Length Organism Details
pol protein A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Fragment: HIV-1 PROTEASE
Mutation: Q7K, L10I, I13V, L33I, S37N, R41K, M46I, L63I, C67A, V82F, I84V, L90M, C95A
Gene Name(s): pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DR7
Query on DR7

A (3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)- 8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4- (2-PYRIDINYL)PHENYL]METHYL]-2,5,6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER
9,,4S (Synonym)
C38 H52 N6 O7
AXRYRYVKAWYZBR-GASGPIRDSA-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)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DR7 Kd: 0.4 nM (85) BindingDB
Ki: 0.009 - 1.1 nM (85 - 89) BindingDB

IC50: 12 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.235
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.38 α = 90.00
b = 58.21 β = 90.00
c = 61.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-02-04
  • Released Date: 2007-02-20
  • Deposition author(s): Klei, H.E., Sheriff, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4