2R8N

Structural Analysis of the Unbound Form of HIV-1 Subtype C Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High-resolution structure of unbound human immunodeficiency virus 1 subtype C protease: implications of flap dynamics and drug resistance.

Coman, R.M.Robbins, A.H.Goodenow, M.M.Dunn, B.M.McKenna, R.

(2008) Acta Crystallogr D Biol Crystallogr 64: 754-763

  • DOI: 10.1107/S090744490801278X
  • Primary Citation of Related Structures:  
    2R8N

  • PubMed Abstract: 
  • The X-ray crystal structure of the unbound state of human immunodeficiency virus 1 (HIV-1) subtype C protease (C PR) has been determined to 1.20 angstroms resolution in the tetragonal space group P4(1)2(1)2, with one monomer per asymmetric unit and u ...

    The X-ray crystal structure of the unbound state of human immunodeficiency virus 1 (HIV-1) subtype C protease (C PR) has been determined to 1.20 angstroms resolution in the tetragonal space group P4(1)2(1)2, with one monomer per asymmetric unit and unit-cell parameters a = 46.7, c = 100.8 angstroms, allowing full anisotropic least-squares refinement. The refined model has a conventional R factor of 14.1% for all reflections and estimated standard deviations in bond lengths and angles for all main-chain non-H atoms of 0.014 angstroms and 0.030 degrees , respectively. The structure is compared with three unbound subtype B proteases (B PRs) to identify structural changes arising from the naturally occurring polymorphisms and delineate their implications in antiretroviral drug resistance/susceptibility. The unbound C PR exhibits a larger distance between the tips of the flaps, a downward displacement of the 36-41 loop and an increased thermal stability of the 10s loop when compared with the B PR structures. The C PR structure presents the highest resolution of the unbound state of a non-subtype-B PR and adds to the understanding of flap dynamics and drug resistance.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32603, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pol proteinA99Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: pol
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for O12158 (Human immunodeficiency virus type 1 group M subtype C (isolate 92BR025))
Explore O12158 
Go to UniProtKB:  O12158
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.711α = 90
b = 46.711β = 90
c = 100.708γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
SCALEPACKdata scaling
CNSrefinement
SHELXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description