3HDK

Crystal structure of chemically synthesized [Aib51/51']HIV-1 protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.

Torbeev, V.Y.Raghuraman, H.Hamelberg, D.Tonelli, M.Westler, W.M.Perozo, E.Kent, S.B.

(2011) Proc.Natl.Acad.Sci.USA 108: 20982-20987

  • DOI: 10.1073/pnas.1111202108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was use ...

    We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the HIV-1 protease in which the flexibility of the "flap" structures (residues 37-61 in each monomer of the homodimeric protein molecule) was systematically varied. These analogue enzymes were further studied by X-ray crystallography, NMR relaxation, and pulse-EPR methods, in conjunction with molecular dynamics simulations. We show that conformational isomerization in the flaps is correlated with structural reorganization of residues in the active site, and that it is preorganization of the active site that is a rate-limiting factor in catalysis.


    Organizational Affiliation

    Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
[Aib51/51']HIV-1 protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Go to UniProtKB:  P03369
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NC
Query on 2NC

Download SDF File 
Download CCD File 
B
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
p2/NC
C35 H68 N11 O8
MQPXOVRKKPPKFZ-QYKDHROSSA-O
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
SMC
Query on SMC
A, B
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
AIB
Query on AIB
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
NLE
Query on NLE
A, B
L-PEPTIDE LINKINGC6 H13 N O2LEU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2NCKd: 17500 nM BINDINGMOAD
2NCKd: 17500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.341α = 90.00
b = 58.395β = 90.00
c = 61.434γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-01-11
    Type: Database references
  • Version 1.3: 2012-12-12
    Type: Other