6GS6 | pdb_00006gs6

Cyclophilin A single mutant D66A in complex with an inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb6GS6/pdb

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


• Deposited: 2018-06-13 Released: 2019-06-26 
• Deposition Author(s): Georgiou, C., De Simone, A., Juarez-Jimenez, J., Walkinshaw, M.D., Michel, J.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A

Juarez-Jimenez, J., Gupta, A.A., Karunanithy, G., May, A., Georgiou, C., Ioannidis, H., De Simone, A., Barlow, P.N., Hulme, A.N., Walkinshaw, M.D., Baldwin, A., Michel, J.

(2020) Chem Sci 

• DOI: https://doi.org/10.1039/C9SC04696H

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.32 kDa 
• Atom Count: 1,505 
• Modelled Residue Count: 160 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A	165	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EA4	B [auth A]	ethyl N-[(4-aminobenzyl)carbamoyl]glycinate C12 H17 N3 O3 UCMPTJMHPJQEED-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EA4	BindingDB:  6GS6	Ki: 1.68e+4 (nM) from 1 assay(s)
		IC50: 1.31e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.01	α = 90
b = 63.01	β = 90
c = 94.72	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
pointless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Georgiou, C., De Simone, A., Juarez-Jimenez, J., Walkinshaw, M.D., Michel, J.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	No. 336289

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description