5E5K

Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 4.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.203 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.

Gerlits, O.Wymore, T.Das, A.Shen, C.H.Parks, J.M.Smith, J.C.Weiss, K.L.Keen, D.A.Blakeley, M.P.Louis, J.M.Langan, P.Weber, I.T.Kovalevsky, A.

(2016) Angew.Chem.Int.Ed.Engl. 55: 4924-4927

  • DOI: 10.1002/anie.201509989
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of en ...

    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.


    Organizational Affiliation

    Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 8 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download SDF File 
Download CCD File 
B
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
Darunavir, TMC114, UIC-94017
C27 H37 N3 O7 S
CJBJHOAVZSMMDJ-HEXNFIEUSA-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: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.593α = 90.00
b = 87.428β = 90.00
c = 46.328γ = 90.00
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.212 
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data reduction
nCNSrefinement
HKL-3000data scaling
LAUEGENdata reduction
LSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2018-06-13
    Type: Data collection, Database references, Derived calculations