2OKN | pdb_00002okn

Crystal Strcture of Human Prolidase

• PDB DOI: https://doi.org/10.2210/pdb2OKN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-17 Released: 2007-02-20 
• Deposition Author(s): Mueller, U., Niesen, F.H., Roske, Y., Goetz, F., Behlke, J., Buessow, K., Heinemann, U., Protein Structure Factory (PSF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Prolidase: The Molecular Basis of PD Disease.

MUELLER, U., NIESEN, F.H., ROSKE, Y., GOETZ, F., BEHLKE, J., BUESSOW, K., HEINEMANN, U.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 109.83 kDa 
• Atom Count: 7,847 
• Modeled Residue Count: 954 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Pro dipeptidase	A, B	494	Homo sapiens	Mutation(s): 1  Gene Names: PEPD, PRD EC: 3.4.13.9
UniProt & NIH Common Fund Data Resources
Find proteins for P12955 (Homo sapiens) Explore P12955  Go to UniProtKB:  P12955
PHAROS:  P12955 GTEx:  ENSG00000124299

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PI	E [auth A], H [auth B], I [auth B]	HYDROGENPHOSPHATE ION H O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-L
MN	C [auth A], D [auth A], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.89	α = 90
b = 108.96	β = 90
c = 212.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Mueller, U., Niesen, F.H., Roske, Y., Goetz, F., Behlke, J., Buessow, K., Heinemann, U., Protein Structure Factory (PSF)

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.6: 2024-10-16
  Changes: Structure summary