2ALF | pdb_00002alf

crystal structure of human CypA mutant K131A

PDB DOI: https://doi.org/10.2210/pdb2ALF/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-08-05 Released: 2005-08-23
Deposition Author(s): Hu, H., Huang, C.-Q., Liu, H.-L., Han, Y., Chen, M.-E., Yu, L., Bi, R.-C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.226 (Depositor)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Nuclease activity of Cyclophilin A and its structural basis

Hu, H., Huang, C.-Q., Liu, H.-L., Han, Y., Chen, M.-E., Yu, L., Bi, R.-C.

To be published.

Macromolecule Content

Total Structure Weight: 17.87 kDa
Atom Count: 1,500
Modeled Residue Count: 164
Deposited Residue Count: 164
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	164	Homo sapiens	Mutation(s): 1 Gene Names: CyPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937 Go to UniProtKB: P62937
PHAROS: P62937 GTEx: ENSG00000196262
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62937
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.226 (Depositor)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.585	α = 90
b = 68.264	β = 90
c = 137.794	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-08-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-08-23
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-11-10
Changes: Database references, Derived calculations
Version 1.5: 2024-05-29
Changes: Data collection

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.