1PSA

STRUCTURE OF A PEPSIN(SLASH)RENIN INHIBITOR COMPLEX REVEALS A NOVEL CRYSTAL PACKING INDUCED BY MINOR CHEMICAL ALTERATIONS IN THE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of a pepsin/renin inhibitor complex reveals a novel crystal packing induced by minor chemical alterations in the inhibitor.

Chen, L.Erickson, J.W.Rydel, T.J.Park, C.H.Neidhart, D.Luly, J.Abad-Zapatero, C.

(1992) Acta Crystallogr.,Sect.B 48: 476-488


  • PubMed Abstract: 
  • The structure determination by molecular replacement methods of a monoclinic pepsin/renin inhibitor complex crystal, with two molecules in the asymmetric unit, is presented. The atomic model, consisting of two liganded pepsin molecules and 110 water ...

    The structure determination by molecular replacement methods of a monoclinic pepsin/renin inhibitor complex crystal, with two molecules in the asymmetric unit, is presented. The atomic model, consisting of two liganded pepsin molecules and 110 water molecules, has been refined to a final crystallographic R value of 0.139 for data between 8 and 2.9 A resolution. The structure reveals a previously undescribed pepsin dimer formed predominantly by polar interactions. Inhibitor binding induces global structural changes in the native enzyme similar, but not identical, to the ones observed in other chemically similar pepsin/renin inhibitor complexes crystallized in an orthorhombic form. A region of the polypeptide chain (residues 292-297) which was not visible in the orthorhombic crystal is well ordered in the presently described structure; possibly induced by crystal contacts. The crystal packing of native pepsin is compared with the two different crystal forms of the inhibited enzyme.


    Related Citations: 
    • Inhibitor Binding Induces Structural Changes in Porcine Pepsin
      Abad-Zapatero, C.,Rydel, T.J.,Neidhart, D.J.,Luly, J.,Erickson, J.W.
      (1991) Adv.Exp.Med.Biol. 306: 9
    • Revised 2.3 Angstroms Structure of Porcine Pepsin: Evidence for a Flexible Subdomain
      Abad-Zapatero, C.,Rydel, T.J.,Erickson, J.
      (1990) Proteins 8: 62


    Organizational Affiliation

    Laboratory of Protein Crystallography, Abbott Laboratories, Abbott Park, IL 60064.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPSIN A
A, B
326Sus scrofaGene Names: PGA
EC: 3.4.23.1
Find proteins for P00791 (Sus scrofa)
Go to UniProtKB:  P00791
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0ZL
Query on 0ZL

Download SDF File 
Download CCD File 
A, B
N-(ethoxycarbonyl)-L-leucyl-N-[(1R,2S,3S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methylhexyl]-L-leucinamide
C29 H55 N3 O6
OAFXIYWBKGSXMT-WBAQKLHDSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000378 (0ZL)
Query on PRD_000378
A,BN-(ethoxycarbonyl)-L-leucyl-N-[(1R,2S,3S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methylhexyl]-L-leucinamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.139 
  • Space Group: P 1 1 21
Unit Cell:
Length (Å)Angle (°)
a = 54.100α = 90.00
b = 74.400β = 90.00
c = 76.500γ = 100.80
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    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
  • Version 1.4: 2017-11-29
    Type: Advisory, Derived calculations, Other