1QFS

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

• PDB DOI: https://doi.org/10.2210/pdb1QFS/pdb

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


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

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Experimental Data Snapshot

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

Starting Model: experimental

Literature

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

Fulop, V., Bocskei, Z., Polgar, L.

(1998) Cell 94: 161-170

• PubMed: 9695945 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.19 kDa 
• Atom Count: 6,460 
• Modelled Residue Count: 710 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PROLYL OLIGOPEPTIDASE)	A	710	Sus scrofa	Mutation(s): 0  EC: 3.4.21.26
UniProt
Find proteins for P23687 (Sus scrofa) Explore P23687  Go to UniProtKB:  P23687

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZPR	B [auth A]	N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL C18 H22 N2 O4 ORZXYSPOAVJYRU-HOTGVXAUSA-N

Binding Affinity Annotations
ID	Source	Binding 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
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000692 (ZPR)	B [auth A]	Z-PRO-PROLINAL	Peptide-like / Inhibitor

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 = 70.9	α = 90
b = 99.8	β = 90
c = 110.9	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-02-27
  Changes: Other
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description