7PCJ

X-ray structure of CypA-C52AK125C/CsA/aromatic foldamer complex

• PDB DOI: https://doi.org/10.2210/pdb7PCJ/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens, Tolypocladium inflatum, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-08-03 Released: 2022-07-13 
• Deposition Author(s): Vallade, M., Langlois d'Estaintot, B., Fischer, L., Buratto, J., Savko, M., Huc, I.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.219 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

X-ray structure of a cystein mutant of Cyclophilin A tethered to an aromatic oligoamide foldamer complexed with Cyclosporin A

Fischer, L., Savko, M., Langlois d'Estaintot, B., Buratto, J., Vallade, M., Huc, I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology, mass spectrometry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.45 kDa 
• Atom Count: 3,009 
• Modelled Residue Count: 364 
• Deposited Residue Count: 366 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A, C [auth D]	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclosporin A	B, D [auth E]	11	Tolypocladium inflatum	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic foldamer	E [auth F], F [auth C]	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	B, D [auth E]	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BMT	B, D [auth E]	L-PEPTIDE LINKING	C10 H19 N O3		THR
MLE	B, D [auth E]	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	B, D [auth E]	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	B, D [auth E]	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142	B, D [auth E]	Cyclosporin A	Cyclic peptide / Immunosuppressant

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.219 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.474	α = 90
b = 70.891	β = 102.7
c = 64.09	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Vallade, M., Langlois d'Estaintot, B., Fischer, L., Buratto, J., Savko, M., Huc, I.

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Funding Organization	Location	Grant Number
Other government	France	--

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.0: 2024-09-04
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2024-10-02
  Changes: Atomic model, Data collection, Derived calculations