2IGW | pdb_00002igw

CYCLOPHILIN 3 complexed with DIPEPTIDE GLY-PRO

• PDB DOI: https://doi.org/10.2210/pdb2IGW/pdb

• Classification: ISOMERASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-25 Released: 2007-08-14 
• Deposition Author(s): Kan, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.264 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Experimental Determination of van der Waals Energies in a Biological System.

Wear, M.A., Kan, D., Rabu, A., Walkinshaw, M.D.

(2007) Angew Chem Int Ed Engl 46: 6453-6456

• PubMed: 17654646 
• DOI: https://doi.org/10.1002/anie.200702084
• Primary Citation Related Structures: 
  2IGV, 2IGW

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Organizational Affiliation: 
• The Centre for Translational and Chemical Biology, The University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3JR, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.77 kDa 
• Atom Count: 1,450 
• Modeled Residue Count: 172 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase 3	A	173	Caenorhabditis elegans	Mutation(s): 0  EC: 5.2.1.8
UniProt
Find proteins for P52011 (Caenorhabditis elegans) Explore P52011  Go to UniProtKB:  P52011

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRO	C [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
GLY	B [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.264 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.724	α = 90
b = 62.724	β = 90
c = 122.756	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Kan, D.

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description