3BVB

Cystal structure of HIV-1 Active Site Mutant D25N and inhibitor Darunavir

Structural Biology Knowledgebase: 3BVB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.150

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BVB

Classification: HYDROLASE

Total Structure Weight: 22177.80

Macromolecule Entities
Molecule Chains Length Organism Details
Protease (Retropepsin) A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: Q7K, D25N, L33I, L63I, C67A, C95A
Gene Name(s): gag-pol

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
017
Query on 017

B (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3- YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]- 1-BENZYL-2-HYDROXYPROPYLCARBAMATE
TMC114, (Synonym)
C27 H37 N3 O7 S
CJBJHOAVZSMMDJ-HEXNFIEUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

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 %)
017 N/A in BindingDB
Ka: 3.3e+06 M-1  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.150
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 58.26 α = 90.00
b = 85.91 β = 90.00
c = 46.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-05
  • Released Date: 2008-04-01
  • Deposition author(s): Liu, F., Weber, I.T.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4