2OK3

X-ray structure of human cyclophilin J at 2.0 angstrom

• PDB DOI: https://doi.org/10.2210/pdb2OK3/pdb

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


• Deposited: 2007-01-15 Released: 2008-01-22 
• Deposition Author(s): Xia, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Targeting Cyclophilin J, a novel peptidyl-prolyl isomerase, can induce cellular G1/S arrest and repress the growth of Hepatocellular carcinoma

Chen, J., Chen, S., Huang, L., Zhao, X., Tan, J., Huang, C., Saiyin, H., Zhang, M., Zeng, X., Xi, J., Wan, B., Zhao, Y., Xia, Z., Jiang, H., Yi, Q., Liu, J.O., Yu, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.29 kDa 
• Atom Count: 1,448 
• Modelled Residue Count: 160 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase-like 3	A	161	Homo sapiens	Mutation(s): 0  Gene Names: PPIL3b EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2H8 (Homo sapiens) Explore Q9H2H8  Go to UniProtKB:  Q9H2H8
PHAROS:  Q9H2H8 GTEx:  ENSG00000240344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth A], C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.577	α = 90
b = 40.577	β = 90
c = 170.682	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-22 
Deposition Author(s): Xia, Z.

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description