1QRP

Human pepsin 3A in complex with a phosphonate inhibitor IVA-VAL-VAL-LEU(P)-(O)PHE-ALA-ALA-OME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural study of the complex between human pepsin and a phosphorus-containing peptidic -transition-state analog.

Fujinaga, M.Cherney, M.M.Tarasova, N.I.Bartlett, P.A.Hanson, J.E.James, M.N.

(2000) Acta Crystallogr.,Sect.D 56: 272-279


  • PubMed Abstract: 
  • The refined crystal structure of the complex between human pepsin and a synthetic phosphonate inhibitor, Iva-Val-Val-Leu(P)-(O)Phe-Ala-Ala-OMe [Iva = isovaleryl, Leu(P) = the phosphinic acid analog of L-leucine, (O)Phe = L-3-phenyllactic acid, OMe = ...

    The refined crystal structure of the complex between human pepsin and a synthetic phosphonate inhibitor, Iva-Val-Val-Leu(P)-(O)Phe-Ala-Ala-OMe [Iva = isovaleryl, Leu(P) = the phosphinic acid analog of L-leucine, (O)Phe = L-3-phenyllactic acid, OMe = methyl ester], is presented. The structure was refined using diffraction data between 30 and 1.96 A resolution to a final R factor ( summation operator| |F(o)| - |F(c)| | / summation operator|F(o)|, where |F(o)| and |F(c)| are the observed and calculated structure-factor amplitudes, respectively) of 20.0%. The interactions of the inhibitor with the enzyme show the locations of the binding sites on the enzyme from S4 to S3'. Modeling of the inhibitor binding to porcine pepsin shows very similar binding sites, except at S4. Comparison of the complex structure with the structures of related inhibitors bound to penicillopepsin helps to rationalize the observed differences in the binding constants. The convergence of reaction mechanisms and geometries in different families of proteinases is also discussed.


    Related Citations: 
    • Crystal structure of human pepsin and its complex with pepstatin
      Fujinaga, M.,Chernaia, M.M.,Tarasova, N.I.,Mosimann, S.C.,James, M.N.G.
      (1995) Protein Sci. 4: 960


    Organizational Affiliation

    Medical Research Council of Canada Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPSIN 3A
E
326Homo sapiensMutation(s): 0 
Gene Names: PGA4
EC: 3.4.23.1
Find proteins for P0DJD7 (Homo sapiens)
Go to Gene View: PGA4
Go to UniProtKB:  P0DJD7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HH0
Query on HH0

Download SDF File 
Download CCD File 
E
methyl N-[(2S)-2-({(S)-hydroxy[(1R)-3-methyl-1-{[N-(3-methylbutanoyl)-L-valyl-L-valyl]amino}butyl]phosphoryl}oxy)-3-phenylpropanoyl]-L-alanyl-L-alaninate
IVA-VAL-VAL-LEU(P)-(O)PHE-ALA-ALA-OME
C36 H60 N5 O10 P
CEPZPGMVMASQKU-ORDNGIEBSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000657 (HH0)
Query on PRD_000657
EIVA VAL VAL P0L ALA MAPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.900α = 90.00
b = 151.270β = 90.00
c = 40.790γ = 90.00
Software Package:
Software NamePurpose
SDMSdata scaling
SDMSdata reduction
GROMOS87refinement
XTALVIEWrefinement
SDMSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    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