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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.237 (Depositor), 0.228 (DCC)
R-Value Work:
0.199 (Depositor), 0.193 (DCC)

Starting Model: experimental
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This is version 1.5 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14832
Sequence Annotations Expand
Reference Sequence

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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 Query on PRD_000424	B	ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARINN	Peptide-like / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.237 (Depositor), 0.228 (DCC)
R-Value Work: 0.199 (Depositor), 0.193 (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

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Entry History

Deposition Data

Released Date: 2005-06-28

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.