3D3T | pdb_00003d3t

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.258 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

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This is version 1.4 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: https://doi.org/10.1128/JVI.00018-08
  • Primary Citation Related Structures: 
    3D3T

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 22.79 kDa 
  • Atom Count: 1,494 
  • Modeled Residue Count: 206 
  • Deposited Residue Count: 208 
  • Unique protein chains: 2

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 protease
A, B
99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: gag-pol
EC: 3.4.23.16
UniProt
Find proteins for Q90VT5 (Human immunodeficiency virus type 1)
Explore Q90VT5 
Go to UniProtKB:  Q90VT5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90VT5
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
P1-P6 SUBSTRATE PEPTIDEC [auth P]10N/AMutation(s): 0 
UniProt
Find proteins for P12495 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
Explore P12495 
Go to UniProtKB:  P12495
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12495
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.258 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.186α = 90
b = 62.186β = 90
c = 82.099γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2024-02-21
    Changes: Data collection