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 Å

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


  • 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
    • 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
    • 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


    Organizational Affiliation

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




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 P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACETYL-*PEPSTATIN
C
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001057
Query on PRD_001057
CACETYL-PEPSTATINOligopeptide / Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.390α = 90.00
b = 86.700β = 90.00
c = 46.270γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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