Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 18.04 kDa 
• Atom Count: 1458 
• Modelled Residue Count: 165 
• Deposited Residue Count: 165 
• Unique protein chains: 1

1W8V

Enzymatic and structural characterization of non peptide ligand cyclophilin complexes

• PDB DOI: 10.2210/pdb1W8V/pdb

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


• Deposited: 2004-09-28 Released: 2004-09-30 
• Deposition Author(s): Kontopidis, G., Taylor, P., Walkinshaw, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

Literature

Enzymatic and Structural Characterization of Non-Peptide Ligand-Cyclophilin Complexes

Kontopidis, G., Taylor, P., Walkinshaw, M.

(2004) Acta Crystallogr D Biol Crystallogr 60: 479-485

• PubMed: 14993672 
• DOI: 10.1107/S0907444904000174
• Primary Citation of Related Structures:  
  1W8L, 1W8M, 1W8V


• PubMed Abstract: 
  

Piperidine ligands are described that provide the first examples of non-peptidic ligand structures for the cyclophilin family of proteins. Crystal structures of two ligand complexes are compared with the unliganded protein and show ligand-induced changes in side-chain conformation and water binding. A peptidylprolyl cis-trans-isomerase assay showed the dissociation constants of the two ligands to be 320 and 25 mM. This study also provides the first published data for both enzymatic activity and three-dimensional structure for any protein-ligand complex that binds with a high-millimolar dissociation constant. The structures may be of relevance in the field of drug design, as they suggest starting points for the design of larger tighter-binding analogues.

---

Organizational Affiliation: 

Structural Biochemistry Group, Department of Biochemistry, The University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3JR, Scotland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A	A	165	Homo sapiens	Mutation(s): 0  Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.182	α = 90
b = 56.593	β = 90
c = 70.239	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-28 
• Released Date: 2004-09-30 
Deposition Author(s): Kontopidis, G., Taylor, P., Walkinshaw, M.

Revision History  

• Version 1.0: 2004-09-30
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Database references, Source and taxonomy
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation