1A8G

HIV-1 PROTEASE IN COMPLEX WITH SDZ283-910


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2Z4
Query on 2Z4

Download SDF File 
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
SDZ283-910
C46 H59 N5 O9
YRESVHUBNCFVEW-FSYSLULESA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000417 (2Z4)
Query on PRD_000417
AINHIBITOR SDZ283-910Peptide-like / Inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2Z4Ki: 7.4 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.150 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 63.100α = 90.00
b = 63.100β = 90.00
c = 83.600γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
MADNESdata reduction
PROCORdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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