3MUO

APPEP_PEPCLOSE+PP closed state

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

Route of Substrate Entry in Prolyl Endopeptidase

Chiu, T.K., Li, M.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prolyl endopeptidase693Aeromonas caviaeMutation(s): 6 
Gene Names: PROLYL ENDOPEPTIDASE
EC: 3.4.21.26
UniProt
Find proteins for Q9X6R4 (Aeromonas caviae)
Explore Q9X6R4 
Go to UniProtKB:  Q9X6R4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6R4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZPR
Query on ZPR
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL
C18 H22 N2 O4
ORZXYSPOAVJYRU-HOTGVXAUSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 3
IDChains NameType/Class2D Diagram3D Interactions
PRD_000692 (ZPR)
Query on PRD_000692		C [auth A],
D [auth A]		Z-PRO-PROLINALPeptide-like / Inhibitor
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
B
sucroseOligosaccharide / Nutrient
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.77α = 90
b = 107.77β = 90
c = 147.22γ = 120
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2011-06-29 
    • Deposition Author(s): Chiu, T.K.

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary