2WFJ

Atomic resolution crystal structure of the PPIase domain of human cyclophilin G in complex with cyclosporin A.

• PDB DOI: https://doi.org/10.2210/pdb2WFJ/pdb

• Classification: ISOMERASE/IMMUNOSUPPRESSANT
• Organism(s): Homo sapiens, Tolypocladium inflatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-06 Released: 2009-06-16 
• Deposition Author(s): Stegmann, C.M., Sheldrick, G.M., Wahl, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.75 Å
• R-Value Free: 0.129 
• R-Value Observed: 0.111 

Literature

The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction.

Stegmann, C.M., Seeliger, D., Sheldrick, G.M., De Groot, B.L., Wahl, M.C.

(2009) Angew Chem Int Ed Engl 48: 5207

• PubMed: 19499554 
• DOI: https://doi.org/10.1002/anie.200900481
• Primary Citation of Related Structures:  
  2WFI, 2WFJ


• PubMed Abstract: 
  

  Water molecules doing time: Atomic-resolution crystal structures of the PPIase domain of cyclophilin G, alone and in complex with cyclosporin A, and together with MD simulations and calorimetry, reveal how trapped water molecules influence the thermodynamic profile of a protein-ligand interaction.

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Organizational Affiliation: 

Research Group X-ray Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 21.21 kDa 
• Atom Count: 1,834 
• Modelled Residue Count: 183 
• Deposited Residue Count: 190 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G	A	179	Homo sapiens	Mutation(s): 0  EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13427 (Homo sapiens) Explore Q13427  Go to UniProtKB:  Q13427
PHAROS:  Q13427 GTEx:  ENSG00000138398

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	B	11	Tolypocladium inflatum	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
BMT	B	L-PEPTIDE LINKING	C10 H19 N O3		THR
MLE	B	L-PEPTIDE LINKING	C7 H15 N O2		LEU
MVA	B	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	B	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	Cyclosporin A	Cyclic peptide / Immunosuppressant

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.75 Å
• R-Value Free: 0.129 
• R-Value Observed: 0.111 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.319	α = 90
b = 64.913	β = 90
c = 69.285	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Stegmann, C.M., Sheldrick, G.M., Wahl, M.C.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
• Version 1.2: 2011-11-23
  Changes: Database references
• Version 1.3: 2012-11-30
  Changes: Other
• Version 1.4: 2019-05-22
  Changes: Data collection, Derived calculations, Other, Refinement description