2OJU | pdb_00002oju

X-ray structure of complex of human cyclophilin J with cyclosporin A

• PDB DOI: https://doi.org/10.2210/pdb2OJU/pdb

• Classification: ISOMERASE/IMMUNOSUPPRESSANT
• Organism(s): Homo sapiens, Tolypocladium inflatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-01-14 Released: 2008-01-22 
• Deposition Author(s): Xia, Z., Huang, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.237 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.94 kDa 
• Atom Count: 2,794 
• Modeled Residue Count: 351 
• Deposited Residue Count: 356 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 3	A, B	167	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	C, D	11	Tolypocladium inflatum	Mutation(s): 0

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	C, D	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BMT	C, D	L-PEPTIDE LINKING	C10 H19 N O3		THR
DAL	C, D	D-PEPTIDE LINKING	C3 H7 N O2		--
MLE	C, D	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	C, D	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	C, D	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142	C, D	Cyclosporin A	Cyclic peptide / Immunosuppressant

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.237 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.387	α = 90
b = 64.387	β = 90
c = 200.943	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2012-12-12
  Changes: Other
• Version 1.5: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection, Derived calculations