1SIV

THREE-DIMENSIONAL STRUCTURE OF A SIV PROTEASE(SLASH)INHIBITOR COMPLEX. IMPLICATIONS FOR THE DESIGN OF HIV-1 AND HIV-2 PROTEASE INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Three-dimensional structure of a simian immunodeficiency virus protease/inhibitor complex. Implications for the design of human immunodeficiency virus type 1 and 2 protease inhibitors.

Zhao, B.Winborne, E.Minnich, M.D.Culp, J.S.Debouck, C.Abdel-Meguid, S.S.

(1993) Biochemistry 32: 13054-13060

  • DOI: https://doi.org/10.1021/bi00211a015
  • Primary Citation of Related Structures:  
    1SIV

  • PubMed Abstract: 

    Simian immunodeficiency virus (SIV) proteins have considerable amino acid sequence homology to those from human immunodeficiency virus (HIV); thus monkeys are considered useful models for the preclinical evaluation of acquired immune deficiency syndrome (AIDS) therapeutics. We have crystallized and determined the three-dimensional structure of SIV protease bound to the hydroxyethylene isostere inhibitor SKF107457. Crystals of the complex were grown from 25-32% saturated sodium chloride, by the hanging drop method of vapor diffusion. They belong to the orthorhombic space group I222, with a = 46.3 A, b = 101.5 A, and c = 118.8 A. The structure has been determined at 2.5-A resolution by molecular replacement and refined to a crystallographic discrepancy factor, R (= sigma parallel Fo magnitude of - magnitude of Fc parallel/sigma magnitude of Fo magnitude of), of 0.189. The overall structure of the complex is very similar to previously reported structures of HIV-1 protease bound to inhibitors. The inhibitor is bound in a conformation that is almost identical to that found for the same inhibitor bound to HIV-1 protease, except for an overall translation of the inhibitor, varying along the backbone atoms from about 1.0 A at the termini to about 0.5 A around the scissile bond surrogate. The structures of the SIV and HIV-1 proteins vary significantly only in three surface loops composed of amino acids 15-20, 34-45, and 65-70. Superposition of the 1188 protein backbone atoms from the two structures gives an rms deviation of 1.0 A; this number is reduced to 0.6 A when atoms from the three surface loops are eliminated from the rms calculation.(ABSTRACT TRUNCATED AT 250 WORDS)


  • Organizational Affiliation

    Department of Macromolecular Sciences, SmithKline Beecham, King of Prussia, Pennsylvania 19406.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIV PROTEASE
A, B
99Simian immunodeficiency virusMutation(s): 0 
UniProt
Find proteins for P05896 (Simian immunodeficiency virus (isolate Mm142-83))
Explore P05896 
Go to UniProtKB:  P05896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05896
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PSI
Query on PSI

Download Ideal Coordinates CCD File 
C [auth B]methyl N-{(4S,5S)-5-[(L-alanyl-L-alanyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-valyl-L-valinate
C29 H47 N5 O7
IUDCAKKZLXFOQA-QJAPXLAMSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PSI Binding MOAD:  1SIV Ki: 8.4 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.3α = 90
b = 101.5β = 90
c = 118.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    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: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Derived calculations