3D3T

Crystal Structure of HIV-1 CRF01_AE in complex with the substrate p1-p6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6.

Bandaranayake, R.M.Prabu-Jeyabalan, M.Kakizawa, J.Sugiura, W.Schiffer, C.A.

(2008) J.Virol. 82: 6762-6766

  • DOI: 10.1128/JVI.00018-08

  • PubMed Abstract: 
  • The effect of amino acid variability between human immunodeficiency virus type 1 (HIV-1) clades on structure and the emergence of resistance mutations in HIV-1 protease has become an area of significant interest in recent years. We determined the fir ...

    The effect of amino acid variability between human immunodeficiency virus type 1 (HIV-1) clades on structure and the emergence of resistance mutations in HIV-1 protease has become an area of significant interest in recent years. We determined the first crystal structure of the HIV-1 CRF01_AE protease in complex with the p1-p6 substrate to a resolution of 2.8 A. Hydrogen bonding between the flap hinge and the protease core regions shows significant structural rearrangements in CRF01_AE protease compared to the clade B protease structure.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A, B
99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag-pol
Find proteins for Q90VT5 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q90VT5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P1-P6 SUBSTRATE PEPTIDE
P
10Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)Mutation(s): 0 
Gene Names: gag
Find proteins for P12495 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Go to UniProtKB:  P12495
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.186α = 90.00
b = 62.186β = 90.00
c = 82.099γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description