1VDN | pdb_00001vdn

Crystal Structure Of Yeast Cyclophilin A Complexed With ACE-Ala-Ala-Pro-Ala-7-Amino-4-Methylcoumarin

• PDB DOI: https://doi.org/10.2210/pdb1VDN/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-24 Released: 2005-06-28 
• Deposition Author(s): Konno, M., Shibano, T., Okudaira, K., Takahashi, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.237 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.191 (DCC) 

Starting Model: experimental

Literature

Crystal Structure Of Yeast Cyclophilin A Complexed With ACE-Ala-Ala-Pro-Ala-7-Amino-4-Methylcoumarin

Konno, M., Shibano, T., Okudaira, K., Takahashi, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.92 kDa 
• Atom Count: 1,444 
• Modeled Residue Count: 167 
• Deposited Residue Count: 168 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclophilin A	A	162	Saccharomyces cerevisiae	Mutation(s): 0  EC: 5.2.1.8
UniProt
Find proteins for P14832 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14832  Go to UniProtKB:  P14832

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
(ACE)AAPA(MCM)	B	6	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000424	B	ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARINN	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.237 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.191 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.737	α = 90
b = 40.009	β = 90
c = 112.736	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Konno, M., Shibano, T., Okudaira, K., Takahashi, N.

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Derived calculations, Structure summary