2WFJ

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G A179Homo sapiensMutation(s): 0 
Gene Names: PPIG
EC: 5.2.1.8
Find proteins for Q13427 (Homo sapiens)
Explore Q13427 
Go to UniProtKB:  Q13427
NIH Common Fund Data Resources
PHAROS:  Q13427
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOSPORIN A B11Tolypocladium inflatumMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
BL-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
BL-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
BL-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
BL-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
BPEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
BCyclosporin ACyclic 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 = 37.319α = 90
b = 64.913β = 90
c = 69.285γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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