2Z6W

Crystal structure of human cyclophilin D in complex with cyclosporin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Crystal Structure of Human Cyclophilin D in Complex with its Inhibitor, Cyclosporin a at 0.96-A Resolution.

Kajitani, K.Fujihashi, M.Kobayashi, Y.Shimizu, S.Tsujimoto, Y.Miki, K.

(2008) Proteins 70: 1635


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
A, B
165Homo sapiensMutation(s): 1 
Gene Names: PPIFCYP3
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens)
Explore P30405 
Go to UniProtKB:  P30405
PHAROS:  P30405
GTEx:  ENSG00000108179 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30405
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLOSPORIN AC [auth M],
D [auth N]
11Tolypocladium inflatumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
C [auth M],
D [auth N]
L-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
C [auth M],
D [auth N]
L-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
C [auth M],
D [auth N]
L-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
C [auth M],
D [auth N]
L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
C [auth M],
D [auth N]
PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.882α = 90
b = 69.313β = 90
c = 112.077γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-11-15
    Changes: Data collection, Derived calculations