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: 2.5 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 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


  • 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 syndr ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIV PROTEASE
A, B
99Simian immunodeficiency virus (isolate Mm142-83)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P05896 (Simian immunodeficiency virus (isolate Mm142-83))
Go to UniProtKB:  P05896
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PSI
Query on PSI

Download SDF File 
Download CCD File 
B
methyl N-{(4S,5S)-5-[(L-alanyl-L-alanyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-valyl-L-valinate
SKF 107457
C29 H47 N5 O7
IUDCAKKZLXFOQA-QJAPXLAMSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000320 (PSI)
Query on PRD_000320
BAla-Ala-Phe.psi.[CH(OH)CH2]Gly-Val-Val-OCH3Peptide-like / Enzyme inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PSIKi: 8.4 nM BINDINGMOAD
GLIKi: 8.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.189 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 46.300α = 90.00
b = 101.500β = 90.00
c = 118.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    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
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other