1QFS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 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

  • Primary Citation of Related Structures:  
  • Also Cited By: 1O6G, 1O6F, 1H2Z, 1H2X, 1VZ3, 1VZ2, 1UOQ, 1UOP, 1UOO, 1H2Y, 1H2W, 1E8N, 1E8M, 1E5T

  • 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 re ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PROLYL OLIGOPEPTIDASE)
A
710Sus scrofaMutation(s): 0 
Gene Names: PREP
EC: 3.4.21.26
Find proteins for P23687 (Sus scrofa)
Go to Gene View: PREP
Go to UniProtKB:  P23687
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZPR
Query on ZPR

Download SDF File 
Download CCD File 
A
N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL
Z-PRO-PROLINAL
C18 H22 N2 O4
ORZXYSPOAVJYRU-HOTGVXAUSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000692 (ZPR)
Query on PRD_000692
AZ-PRO-PROLINALPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZPRIC50: 0.3 - 54 nM (100) BINDINGDB
ZPRKi: 0.2 - 0.3 nM (97) BINDINGDB
ZPRIC50: 0.33 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.900α = 90.00
b = 99.800β = 90.00
c = 110.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
CCP4model building
CCP4phasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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