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 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDYL-PROLYL CIS-TRANS ISOMERASEA, B165Homo 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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLOSPORIN AC [auth M], D [auth N]11Tolypocladium inflatumMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D 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
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000142
Query on PRD_000142
C [auth M], D [auth N]Cyclosporin ACyclic peptide /  Immunosuppressant Ligand Interaction
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