1A8G

HIV-1 PROTEASE IN COMPLEX WITH SDZ283-910


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-ray structure and conformational dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: agreement of time-resolved spectroscopy and molecular dynamics simulations.

Ringhofer, S.Kallen, J.Dutzler, R.Billich, A.Visser, A.J.Scholz, D.Steinhauser, O.Schreiber, H.Auer, M.Kungl, A.J.

(1999) J Mol Biol 286: 1147-1159

  • DOI: 10.1006/jmbi.1998.2533
  • Primary Citation of Related Structures:  
    1A8G

  • PubMed Abstract: 
  • Based on the X-ray structure of the human immunodeficiency virus type-1 (HIV-1) protease in complex with the statine-derived inhibitor SDZ283-910, a 542 ps molecular dynamics trajectory was computed. For comparison with the 805 ps trajectory obtained ...

    Based on the X-ray structure of the human immunodeficiency virus type-1 (HIV-1) protease in complex with the statine-derived inhibitor SDZ283-910, a 542 ps molecular dynamics trajectory was computed. For comparison with the 805 ps trajectory obtained for the uncomplexed enzyme, the theoretical fluorescence anisotropy decay of the unliganded protease and the inhibitor complex was calculated from the trajectories of the Trp6A/Trp6B and Trp42A/Trp42B transition dipole moments. This enabled us to directly compare the simulated data with the experimental picosecond time-resolved fluorescence data. Fitting both experimental and simulated data to the Kohlrausch-Williams-Watts (KWW) function exp(-t/tauk)beta revealed a very good agreement for the uncomplexed protease as well as for the SDZ283-910 complex. Binding of the inhibitor induced a faster decay of both the experimental and the computed protease fluorescence anisotropy decay. By this integrative approach, the atomic detail of inhibitor-induced changes in the conformational dynamics of the HIV-1 protease was experimentally verified and will be used for further inhibitor optimisation.


    Organizational Affiliation

    Institut für Theoretische Chemie, Universität Wien, Währingerstr. 17, Wien, A-1090, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEAB99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16 (PDB Primary Data), 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 P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2Z4
Query on 2Z4

Download CCD File 
A
benzyl [(1R)-1-({(1S,2S,3S)-1-benzyl-2-hydroxy-4-({(1S)-1-[(2-hydroxy-4-methoxybenzyl)carbamoyl]-2-methylpropyl}amino)-3-[(4-methoxybenzyl)amino]-4-oxobutyl}carbamoyl)-2,2-dimethylpropyl]carbamate
C46 H59 N5 O9
YRESVHUBNCFVEW-FSYSLULESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2Z4Ki:  7.400000095367432   nM  Binding MOAD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000417 (2Z4)
Query on PRD_000417
AINHIBITOR SDZ283-910Peptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.1α = 90
b = 63.1β = 90
c = 83.6γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
PROCORdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2018-04-18
    Changes: Data collection, Other