7HVP

X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A COMPLEX BETWEEN A SYNTHETIC PROTEASE OF HUMAN IMMUNODEFICIENCY VIRUS 1 AND A SUBSTRATE-BASED HYDROXYETHYLAMINE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor.

Swain, A.L.Miller, M.M.Green, J.Rich, D.H.Schneider, J.Kent, S.B.Wlodawer, A.

(1990) Proc.Natl.Acad.Sci.USA 87: 8805-8809


  • PubMed Abstract: 
  • The structure of a crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site has been determined. The sequence of the inhibitor JG-365 is Ac-Ser-Leu-Asn-Phe ...

    The structure of a crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site has been determined. The sequence of the inhibitor JG-365 is Ac-Ser-Leu-Asn-Phe-psi[CH(OH)CH2N]-Pro-Ile-Val-OMe; the Ki is 0.24 nM. The hydroxyethylamine moiety, in place of the normal scissile bond of the substrate, is believed to mimic a tetrahedral reaction intermediate. The structure of the complex has been refined to an R factor of 0.146 at 2.4-A resolution by using restrained least squares with rms deviations in bond lengths of 0.02 A and bond angles of 4. The bound inhibitor diastereomer has the S configuration at the hydroxyethylamine chiral carbon, and the hydroxyl group is positioned between the active site aspartate carboxyl groups within hydrogen bonding distance. Comparison of this structure with a reduced peptide bond inhibitor-protease complex indicates that these contacts confer the exceptional binding strength of JG-365.


    Related Citations: 
    • Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family
      Miller, M.,Jaskolski, M.,Rao, J.K.M.,Leis, J.,Wlodawer, A.
      (1989) Nature 337: 576
    • Enzymatic Activity of a Synthetic 99 Residue Protein Corresponding to the Putative HIV-1 Protease
      Schneider, J.,Kent, S.B.H.
      (1988) Cell 54: 363
    • Molecular Modeling of the HIV-1 Protease and its Substrate Binding Site
      Weber, I.T.,Miller, M.,Jaskolski, M.,Leis, J.,Skalka, A.M.,Wlodawer, A.
      (1989) Science 243: 928
    • Structure at 2.5-Angstroms Resolution of Chemically Synthesized Human Immunodeficiency Virus Type I Protease Complexed with a Hydroxyethylene-Based Inhibitor
      Jaskolski, M.,Tomasselli, A.G.,Sawyer, T.K.,Staples, D.G.,Heinrikson, R.L.,Schneider, J.,Kent, S.B.,Wlodawer, A.
      (1991) Biochemistry 30: 1600
    • Structure of Complex of Synthetic HIV-1 Protease with a Substrate-Based Inhibitor at 2.3 Angstroms Resolution
      Miller, M.,Schneider, J.,Sathyanarayana, B.K.,Toth, M.V.,Marshall, G.R.,Clawson, L.,Selk, L.,Kent, S.B.H.,Wlodawer, A.
      (1989) Science 246: 1149
    • Conserved Folding in Retroviral Proteases. Crystal Structure of a Synthetic HIV-1 Protease
      Wlodawer, A.,Miller, M.,Jaskolski, M.,Sathyanarayana, B.K.,Baldwin, E.,Weber, I.T.,Selk, L.M.,Clawson, L.,Schneider, J.,Kent, S.B.H.
      (1989) Science 245: 616


    Organizational Affiliation

    Crystallography Laboratory, National Cancer Institute-Frederick Cancer Research and Development Center, MD 21702.




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 BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03369
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INHIBITOR ACE-SER-LEU-ASN-PHE-PSI(CH(OH)-CH2N)-PRO-ILE VME (JG-365)
C
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000228
Query on PRD_000228
CJG-365Peptide-like / Inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.200α = 90.00
b = 58.800β = 90.00
c = 62.000γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    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: 2013-02-27
    Type: Other
  • Version 1.4: 2014-08-06
    Type: Derived calculations
  • Version 1.5: 2017-11-29
    Type: Derived calculations, Other