3MUN | pdb_00003mun

APPEP_PEPCLOSE closed state

• PDB DOI: https://doi.org/10.2210/pdb3MUN/pdb

• Classification: HYDROLASE
• Organism(s): Aeromonas caviae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-05-03 Released: 2011-05-18 
• Deposition Author(s): Chiu, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.206 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Route of Substrate Entry in Prolyl Endopeptidase

Chiu, T.K., Li, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.38 kDa 
• Atom Count: 5,866 
• Modeled Residue Count: 684 
• Deposited Residue Count: 693 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A	693	Aeromonas caviae	Mutation(s): 6  Gene Names: PROLYL ENDOPEPTIDASE EC: 3.4.21.26
UniProt
Find proteins for Q9X6R4 (Aeromonas caviae) Explore Q9X6R4  Go to UniProtKB:  Q9X6R4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.206 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.14	α = 90
b = 108.14	β = 90
c = 147.3	γ = 120

Software Package:

Software Name	Purpose
EPMR	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Chiu, T.K.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• 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