1W8L | pdb_00001w8l

Enzymatic and structural characterization of non peptide ligand cyclophilin complexes

• PDB DOI: https://doi.org/10.2210/pdb1W8L/pdb

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


• Deposited: 2004-09-23 Released: 2004-09-30 
• Deposition Author(s): Kontopidis, G., Taylor, P., Walkinshaw, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1107/S0907444904000174
• Primary Citation 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.

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

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 18.18 kDa 
• Atom Count: 1,474 
• Modeled Residue Count: 165 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A	A	165	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000196262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1P3	B [auth A]	(3R)-1-ACETYL-3-METHYLPIPERIDINE C8 H15 N O XKFPNHDGLSYZRC-SSDOTTSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.09	α = 90
b = 54.31	β = 90
c = 70.97	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

• 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: 2018-06-13
  Changes: Data collection, Database references
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Refinement description