1E8K | pdb_00001e8k

Cyclophilin 3 Complexed With Dipeptide Ala-Pro

• PDB DOI: https://doi.org/10.2210/pdb1E8K/pdb

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


• Deposited: 2000-09-25 Released: 2001-09-20 
• Deposition Author(s): Wu, S.Y., Dornan, J., Kontopidis, G., Taylor, P., Walkinshaw, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

The First Direct Determination of a Ligand Binding Constant in Protein Crystals

Wu Sy, S.Y., Dornan, J., Kontopidis, G., Taylor, P., Walkinshaw, M.D.

(2001) Angew Chem Int Ed Engl 40: 582

• PubMed: 11180378 
• Primary Citation of Related Structures:  
  1E8K

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Organizational Affiliation: 
• Structural Biochemistry Group Institute of Cell and Molecular Biology The University of Edinburgh Michael Swann Building, King's Buildings Mayfield Road, Edinburgh, EH9 3JR (UK).

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.78 kDa 
• Atom Count: 1,546 
• Modeled Residue Count: 173 
• 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
ALA	B [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.035	α = 90
b = 61.035	β = 90
c = 122.66	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-09-20 
Deposition Author(s): Wu, S.Y., Dornan, J., Kontopidis, G., Taylor, P., Walkinshaw, M.D.

Revision History  

• Version 1.0: 2001-09-20
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2013-07-24
  Changes: Derived calculations, Other
• Version 1.3: 2018-06-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Refinement description