2X7K

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

• PDB DOI:  https://doi.org/10.2210/pdb2X7K/pdb

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


• Deposited: 2010-03-01 Released: 2010-03-23 
• Deposition Author(s): Stegmann, C.M., Luehrmann, R., Wahl, M.C.

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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 

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

• PubMed: 20368803 
• DOI: https://doi.org/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 site distinct from its active site.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 19.73 kDa 
• Atom Count: 1,709 
• Modelled Residue Count: 175 
• Deposited Residue Count: 177 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE-LIKE 1	A	166	Homo sapiens	Mutation(s): 0  Gene Names: PPIL1, CYPL1, CGI-124, UNQ2425/PRO4984 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C6 (Homo sapiens) Explore Q9Y3C6  Go to UniProtKB:  Q9Y3C6
PHAROS:  Q9Y3C6

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	C [auth A], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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		Ligand Interaction

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 = 103.218	α = 90
b = 35.701	β = 90
c = 45.851	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Stegmann, C.M., Luehrmann, R., Wahl, M.C.

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