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: 2.40 Å
  • R-Value Observed: 0.146 

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 U S A 87: 8805-8809

  • DOI: 10.1073/pnas.87.22.8805
  • Primary Citation of Related Structures:  
    7HVP

  • 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: 
    • 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
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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



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 (UniProt), 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 P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INHIBITOR ACE-SER-LEU-ASN-PHE-PSI(CH(OH)-CH2N)-PRO-ILE VME (JG-365)C7N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A,BL-PEPTIDE LINKINGC4 H9 N O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000228
Query on PRD_000228
CJG-365Peptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.2α = 90
b = 58.8β = 90
c = 62γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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