6FK1 | pdb_00006fk1

Cyclophilin A

PDB DOI: https://doi.org/10.2210/pdb6FK1/pdb

Classification: ISOMERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-01-23 Released: 2019-02-06
Deposition Author(s): Lisboa, J., dos Santos, N.M.S.
Funding Organization(s): FCT, COMPETE 2020

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.181 (Depositor), 0.180 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Production, crystallization and structure determination of cyclophilin A from Mus musculus

Lisboa, J., dos Santos, N.M.S.

To be published.

Macromolecule Content

Total Structure Weight: 19.19 kDa
Atom Count: 1,442
Modeled Residue Count: 168
Deposited Residue Count: 172
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A	172	Mus musculus	Mutation(s): 0 Gene Names: Ppia EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P17742 (Mus musculus) Explore P17742 Go to UniProtKB: P17742
IMPC: MGI:97749
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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: 1.30 Å
R-Value Free: 0.181 (Depositor), 0.180 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.717	α = 90
b = 61.717	β = 90
c = 93.13	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

dos Santos, N.M.S.

Funding Organization	Location	Grant Number
FCT	Portugal	POCI-01-0145-FEDER-016608
COMPETE 2020	Portugal	Norte-01-0145-FEDER-000012

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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.