1ZLF

Crystal structure of a complex of mutant HIV-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

HIV-1 protease mutations and inhibitor modifications monitored on a series of complexes. Structural basis for the effect of the A71V mutation on the active site

Skalova, T.Dohnalek, J.Duskova, J.Petrokova, H.Hradilek, M.Soucek, M.Konvalinka, J.Hasek, J.

(2006) J.Med.Chem. 49: 5777-5784

  • DOI: 10.1021/jm0605583
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two new X-ray structures of an HIV-1 protease mutant (A71V, V82T, I84V) in complex with inhibitors SE and SQ, pseudotetrapeptide inhibitors with an acyclic S-hydroxyethylamine isostere, were determined. Comparison of eight structures exploring the bi ...

    Two new X-ray structures of an HIV-1 protease mutant (A71V, V82T, I84V) in complex with inhibitors SE and SQ, pseudotetrapeptide inhibitors with an acyclic S-hydroxyethylamine isostere, were determined. Comparison of eight structures exploring the binding of four similar inhibitors--SE, SQ (S-hydroxyethylamine isostere), OE (ethyleneamine), and QF34 (hydroxyethylene)--to wild-type and A71V/V82T/I84V HIV-1 protease elucidates the principles of altered interaction with changing conditions. The A71V mutation, which is distant from the active site, causes changes in the structure of the enzyme detectable by the means of X-ray structure analysis, and a route of propagation of the effect toward the active site is proposed.


    Organizational Affiliation

    Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nam. 2, 162 06 Praha 6, Czech Republic. skalova@imc.cas.cz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASE RETROPEPSIN
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)Human immunodeficiency virus 1
This entity is chimeric
Mutation(s): 3 
Gene Names: gag-pol, pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Find proteins for Q7ZCL6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q7ZCL6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0ZR
Query on 0ZR

Download SDF File 
Download CCD File 
B
N-{(2R,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-glutaminyl-L-phenylalaninamide
C38 H50 N6 O7
SSPOMXWWHDMCTH-XDIGFQIYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000384 (0ZR)
Query on PRD_000384
BBOC-PS0-PHE-GLN-PHE-NH2Peptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0ZRKi: 33 - 1000 nM (96) BINDINGDB
0ZRKi: 1000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.207 
  • Space Group: P 61
  • Diffraction Data DOI: 
    10.15785/SBGRID/721 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 62.777α = 90.00
b = 62.777β = 90.00
c = 83.407γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other