2OK3 | pdb_00002ok3

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.255 (Depositor), 0.252 (DCC)
R-Value Work:
0.202 (Depositor), 0.205 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2OK3

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H2H8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.255 (Depositor), 0.252 (DCC)
R-Value Work: 0.202 (Depositor), 0.205 (DCC)
R-Value Observed: 0.202 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2008-01-22

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.