5T8H

Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with amprenavir at pH 6.0


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K.

Gerlits, O.Keen, D.A.Blakeley, M.P.Louis, J.M.Weber, I.T.Kovalevsky, A.

(2017) J. Med. Chem. 60: 2018-2025

  • DOI: 10.1021/acs.jmedchem.6b01767

  • PubMed Abstract: 
  • HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature jo ...

    HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly alter the drug-enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.


    Related Citations: 
    • Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules.
      Adams, P.D.,Mustyakimov, M.,Afonine, P.V.,Langan, P.
      (2009) Acta Crystallogr. D Biol. Crystallogr. 65: 567


    Organizational Affiliation

    UT/ORNL Joint Institute of Biological Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 8 
Gene Names: pol
Find proteins for Q7SSI0 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q7SSI0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
478
Query on 478

Download SDF File 
Download CCD File 
B
{3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER
Amprenavir
C25 H35 N3 O6 S
YMARZQAQMVYCKC-OEMFJLHTSA-N
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A, B
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.217 
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.234α = 90.00
b = 87.359β = 90.00
c = 46.565γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
LAUEGENdata reduction
HKL-3000data reduction
HKL-3000data scaling
nCNSrefinement
LSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references