1QFS

PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL

  • Classification: HYDROLASE
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 1999-04-13 Released: 1999-05-13 
  • Deposition Author(s): Fulop, V.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis.

Fulop, V.Bocskei, Z.Polgar, L.

(1998) Cell 94: 161-170

  • DOI: 10.1016/s0092-8674(00)81416-6
  • Primary Citation of Related Structures:  
    1QFM, 1QFS

  • PubMed Abstract: 
  • Prolyl oligopeptidase is a large cytosolic enzyme that belongs to a new class of serine peptidases. The enzyme is involved in the maturation and degradation of peptide hormones and neuropeptides, which relate to the induction of amnesia. The 1.4 A resolution crystal structure is presented here ...

    Prolyl oligopeptidase is a large cytosolic enzyme that belongs to a new class of serine peptidases. The enzyme is involved in the maturation and degradation of peptide hormones and neuropeptides, which relate to the induction of amnesia. The 1.4 A resolution crystal structure is presented here. The enzyme contains a peptidase domain with an alpha/beta hydrolase fold, and its catalytic triad (Ser554, His680, Asp641) is covered by the central tunnel of an unusual beta propeller. This domain makes prolyl oligopeptidase an oligopeptidase by excluding large structured peptides from the active site. In this way, the propeller protects larger peptides and proteins from proteolysis in the cytosol. The structure is also obtained with a transition state inhibitor, which may facilitate drug design to treat memory disorders.


    Organizational Affiliation

    Department of Biochemistry, Oxford Centre for Molecular Sciences, University of Oxford, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PROLYL OLIGOPEPTIDASE)A710Sus scrofaMutation(s): 0 
Gene Names: PREP
EC: 3.4.21.26
UniProt
Find proteins for P23687 (Sus scrofa)
Explore P23687 
Go to UniProtKB:  P23687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23687
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZPR
Query on ZPR

Download Ideal Coordinates CCD File 
B [auth A]N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL
C18 H22 N2 O4
ORZXYSPOAVJYRU-HOTGVXAUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZPR BindingDB:  1QFS Ki: min: 0.21, max: 8 (nM) from 7 assay(s)
IC50: min: 0.33, max: 54 (nM) from 4 assay(s)
PDBBind:  1QFS IC50: 0.33 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000692 (ZPR)
Query on PRD_000692
B [auth A]Z-PRO-PROLINALPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.9α = 90
b = 99.8β = 90
c = 110.9γ = 90
Software Package:
Software NamePurpose
CCP4model building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1999-04-13 
  • Released Date: 1999-05-13 
  • Deposition Author(s): Fulop, V.

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other