7QBW | pdb_00007qbw

Human Cyclophilin A double mutant C52AK125C

PDB DOI: https://doi.org/10.2210/pdb7QBW/pdb

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

Deposited: 2021-11-19 Released: 2022-11-30
Deposition Author(s): Fischer, L., Buratto, J., Langlois d'Estaintot, B.
Funding Organization(s): Agence Nationale de la Recherche (ANR), European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.170 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human Cyclophilin A double mutant C52AK125C

Fischer, L., Buratto, J., Langlois d'Estaintot, B.

To be published.

Macromolecule Content

Total Structure Weight: 18.16 kDa
Atom Count: 1,396
Modeled Residue Count: 164
Deposited Residue Count: 165
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	165	Homo sapiens	Mutation(s): 2 Gene Names: PPIA, 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
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.59 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.170 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.3	α = 90
b = 54.24	β = 90
c = 87.29	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-30

Deposition Author(s):

Langlois d'Estaintot, B.

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	European Union	ANR-19-CE07-0034
European Union (EU)	European Union	H2020-MSCA-IF-2016-751019-PROFOLIG

Revision History (Full details and data files)

Version 1.0: 2022-11-30
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.