5HVP

CRYSTALLOGRAPHIC ANALYSIS OF A COMPLEX BETWEEN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE AND ACETYL-PEPSTATIN AT 2.0-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution.

Fitzgerald, P.M.McKeever, B.M.VanMiddlesworth, J.F.Springer, J.P.Heimbach, J.C.Leu, C.T.Herber, W.K.Dixon, R.A.Darke, P.L.

(1990) J Biol Chem 265: 14209-14219

  • Primary Citation of Related Structures:  
    5HVP

  • PubMed Abstract: 
  • The mode of binding of acetyl-pepstatin to the protease from the human immunodeficiency virus type 1 (HIV-1) has been determined by x-ray diffraction analysis. Crystals of an acetyl-pepstatin-HIV-1 protease complex were obtained in space group P2(1)2 ...

    The mode of binding of acetyl-pepstatin to the protease from the human immunodeficiency virus type 1 (HIV-1) has been determined by x-ray diffraction analysis. Crystals of an acetyl-pepstatin-HIV-1 protease complex were obtained in space group P2(1)2(1)2 (unit cell dimensions a = 58.39 A, b = 86.70 A, c = 46.27 A) by precipitation with sodium chloride. The structure was phased by molecular replacement methods, and a model for the structure was refined using diffraction data to 2.0 A resolution (R = 0.176 for 12901 reflections with I greater than sigma (I); deviation of bond distances from ideal values = 0.018 A; 172 solvent molecules included). The structure of the protein in the complex has been compared with the structure of the enzyme without the ligand. A core of 44 amino acids in each monomer, including residues in the active site and residues at the dimer interface, remains unchanged on binding of the inhibitor (root mean square deviation of alpha carbon positions = 0.39 A). The remaining 55 residues in each monomer undergo substantial rearrangement, with the most dramatic changes occurring at residues 44-57 (these residues comprise the so-called flaps of the enzyme). The flaps interact with one another and with the inhibitor so as to largely preserve the 2-fold symmetry of the protein. The inhibitor is bound in two approximately symmetric orientations. In both orientations the peptidyl backbone of the inhibitor is extended; a network of hydrogen bonds is formed between the inhibitor and the main body of the protein as well as between the inhibitor and the flaps. Hydrophobic side chains of residues in the body of the protein form partial binding sites for the side chains of the inhibitor; hydrophobic side chains of residues in the flaps complete these binding sites.


    Related Citations: 
    • Three-Dimensional Structure of Aspartyl Protease from Human Immunodeficiency Virus HIV-1
      Navia, M.A., Fitzgerald, P.M.D., Mckeever, B.M., Leu, C.-T., Heimbach, J.C., Herber, W.K., Sigal, I.S., Darke, P.L., Springer, J.P.
      (1989) Nature 337: 615
    • Crystallization of the Aspartylprotease from the Human Immunodefeciency Virus, HIV-1
      Mckeever, B.M., Navia, M.A., Fitzgerald, P.M.D., Springer, J.P., Leu, C.-T., Heimbach, J.C., Herber, W.K., Sigal, I.S., Darke, P.L.
      (1989) J Biol Chem 264: 1919
    • Human Immunodeficiency Virus Protease. Bacterial Expression and Characterization of the Purified Aspartic Protease
      Darke, P.L., Leu, C.-T., Davis, L.J., Heimabch, J.C., Diehl, R.E., Hill, W.S., Dixon, R.A.F., Sigal, I.S.
      (1989) J Biol Chem 264: 2307

    Organizational Affiliation

    Department of Biophysical Chemistry, Merck Sharp and Dohme Research Laboratories, Rahway, New Jersey 07065.



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 P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYL-*PEPSTATINC6StreptomycesMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001057
Query on PRD_001057
CACETYL-PEPSTATINOligopeptide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.39α = 90
b = 86.7β = 90
c = 46.27γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    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: 2017-11-29
    Changes: Derived calculations, Other