3BXR

Crystal Structures Of Highly Constrained Substrate And Hydrolysis Products Bound To HIV-1 Protease. Implications For Catalytic Mechanism

Structural Biology Knowledgebase: 3BXR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BXR

Classification: HYDROLASE

Total Structure Weight: 22591.68

Macromolecule Entities
Molecule Chains Length Organism Details
Protease A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Fragment: UNP residues 491-589
Mutation: Q7K, D25N, L33I, C67X, C95X
Gene Name(s): gag-pol

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

B (9S,12S)-9-(1-methylethyl)-N-[(8S,11S)-8- [(1S)-1-methylpropyl]-7,10-dioxo-2-oxa-6,9- diazabicyclo[11.2.2]heptadeca-1(15),13,16- trien-11-yl]-7,10-dioxo-2-oxa-8,11-diazabicyclo[12.2.2]octadeca- 1(16),14,17-triene-12-carboxamide
C37 H51 N5 O7
LMXVYRBJYYRIPR-JNGVDVETSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DRR Ki: 800 nM (88) BindingDB

Ki: 800 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
ABA
Query on ABA
A, B L-PEPTIDE LINKING C4 H9 N O2 ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.179
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.93 α = 90.00
b = 58.05 β = 90.00
c = 61.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-14
  • Released Date: 2008-03-25
  • Deposition author(s): Tyndall, J.D., Pattenden, L.K., Reid, R.C., Hu, S.H., Alewood, D., Alewood, P.F., Walsh, T., Fairlie, D.P., Martin, J.L.

Revision History

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