2IW2 | pdb_00002iw2

Crystal structure of human Prolidase

• PDB DOI: https://doi.org/10.2210/pdb2IW2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-24 Released: 2006-07-05 
• Deposition Author(s): Mueller, U., Niesen, F.H., Roske, Y., Goetz, F., Behlke, J., Buessow, K., Heinemann, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 109.44 kDa 
• Atom Count: 8,501 
• Modeled Residue Count: 956 
• 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): 0  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.579	α = 90
b = 108.518	β = 90
c = 211.024	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE/RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-05 
Deposition Author(s): Mueller, U., Niesen, F.H., Roske, Y., Goetz, F., Behlke, J., Buessow, K., Heinemann, U.

Revision History  

• Version 1.0: 2006-07-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary