2X7K

The crystal structure of PPIL1 in complex with cyclosporine A suggests a binding mode for SKIP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Crystal Structure of Ppil1 Bound to Cyclosporine a Suggests a Binding Mode for a Linear Epitope of the Skip Protein.

Stegmann, C.M.Luehrmann, R.Wahl, M.C.

(2010) PLoS One 5: 13

  • DOI: 10.1371/journal.pone.0010013
  • Primary Citation of Related Structures:  
    2X7K

  • PubMed Abstract: 
  • The removal of introns from pre-mRNA is carried out by a large macromolecular machine called the spliceosome. The peptidyl-prolyl cis/trans isomerase PPIL1 is a component of the human spliceosome and binds to the spliceosomal SKIP protein via a binding s ...

    The removal of introns from pre-mRNA is carried out by a large macromolecular machine called the spliceosome. The peptidyl-prolyl cis/trans isomerase PPIL1 is a component of the human spliceosome and binds to the spliceosomal SKIP protein via a binding site distinct from its active site.


    Organizational Affiliation

    Max-Planck-Institut für biophysikalische Chemie, Zelluläre Biochemie/Makromolekulare Röntgenkristallographie, Göttingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 1 A166Homo sapiensMutation(s): 0 
Gene Names: PPIL1CYPL1CGI-124UNQ2425/PRO4984
EC: 5.2.1.8
Find proteins for Q9Y3C6 (Homo sapiens)
Explore Q9Y3C6 
Go to UniProtKB:  Q9Y3C6
NIH Common Fund Data Resources
PHAROS:  Q9Y3C6
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOSPORIN A B11Tolypocladium inflatumMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-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

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.149 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.218α = 90
b = 35.701β = 90
c = 45.851γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-10-16
    Changes: Data collection, Experimental preparation, Other