1QFM | pdb_00001qfm

PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE

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

  • Deposited: 1999-04-12 Released: 1999-05-13 
  • Deposition Author(s): Fulop, V.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.206 (Depositor) 
  • R-Value Work: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1QFM

This is version 1.5 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: https://doi.org/10.1016/s0092-8674(00)81416-6
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 81.81 kDa 
  • Atom Count: 6,645 
  • Modeled Residue Count: 710 
  • Deposited Residue Count: 710 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (PROLYL OLIGOPEPTIDASE)710Sus scrofaMutation(s): 0 
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
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
CSX
Query on CSX
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.206 (Depositor) 
  • R-Value Work:  0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.7α = 90
b = 99.6β = 90
c = 110.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
SHARPphasing
X-PLORrefinement
CCP4phasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • 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: Non-polymer description, Version format compliance
  • Version 1.3: 2011-09-14
    Changes: Other
  • Version 1.4: 2014-11-12
    Changes: Non-polymer description
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations