Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 18.15 kDa 
• Atom Count: 1549 
• Modelled Residue Count: 165 
• Deposited Residue Count: 165 
• Unique protein chains: 1

5LUD

Structure of Cyclophilin A in complex with 2,3-Diaminopyridine

• DOI: 10.2210/pdb5LUD/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-08 Released: 2017-04-05 
• Deposition Author(s): McNae, I.W., Nowicki, M.W., Blackburn, E.A., Wear, M.A., Walkinshaw, M.D.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using BiacoreTM T200.

Wear, M.A., Nowicki, M.W., Blackburn, E.A., McNae, I.W., Walkinshaw, M.D.

(2017) FEBS Open Bio 7: 533-549

• PubMed: 28396838 
• DOI: 10.1002/2211-5463.12201
• Primary Citation of Related Structures:  
  5LUD


• PubMed Abstract: 
  

We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his-tagged human cyclophilin-A. Our orientation-specific stabilisation approach captures his-tagged protein under 'physiological conditions' (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni ²⁺ -nitrilotriacetic acid surfaces, very briefly activated for primary amine-coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin-A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo-kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin-A-cyclosporin-A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin-A, from a screen of a fragment library. This fragment, 2,3-diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X-ray structure of this 109-Da fragment bound in the active site of cyclophilin-A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin-A inhibitors.

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Organizational Affiliation: 

The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A	165	Homo sapiens	Mutation(s): 0  Gene Names: HEL-S-69p, PPIA, CYPA EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS:  P62937 GTEx:  ENSG00000196262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
76X	A	pyridine-2,3-diamine C5 H7 N3 ZZYXNRREDYWPLN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.535	α = 90
b = 54.477	β = 90
c = 86.808	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-08 
• Released Date: 2017-04-05 
Deposition Author(s): McNae, I.W., Nowicki, M.W., Blackburn, E.A., Wear, M.A., Walkinshaw, M.D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	081287/Z/06/Z
Wellcome Trust	United Kingdom	101527/Z/13/Z

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-04-19
  Changes: Database references