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- PDB-1ikf: A CONFORMATION OF CYCLOSPORIN A IN AQUEOUS ENVIRONMENT REVEALED B... -

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Basic information

Entry
Database: PDB / ID: 1ikf
TitleA CONFORMATION OF CYCLOSPORIN A IN AQUEOUS ENVIRONMENT REVEALED BY THE X-RAY STRUCTURE OF A CYCLOSPORIN-FAB COMPLEX
Components
  • CYCLOSPORIN ACiclosporin
  • IGG1-KAPPA R45-45-11 FAB (HEAVY CHAIN)
  • IGG1-KAPPA R45-45-11 FAB (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM/IMMUNOSUPPRESSANT / IMMUNE SYSTEM-IMMUNOSUPPRESSANT COMPLEX / FAB-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Cyclosporin A / :
Function and homology information
Biological speciesHOMO SAPIENS (human)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsVix, O. / Altschuh, D. / Rees, B. / Thierry, J.-C.
Citation
Journal: Science / Year: 1992
Title: A Conformation of Cyclosporin a in Aqueous Environment Revealed by the X-Ray Structure of a Cyclosporin-Fab Complex.
Authors: Altschuh, D. / Vix, O. / Rees, B. / Thierry, J.C.
#1: Journal: Proteins / Year: 1993
Title: Crystallographic Analysis of the Interaction between Cyclosporin a and the Fab Fragment of a Monoclonal Antibody.
Authors: Vix, O. / Rees, B. / Thierry, J.C. / Altschuh, D.
History
DepositionDec 9, 1993-
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-KAPPA R45-45-11 FAB (LIGHT CHAIN)
H: IGG1-KAPPA R45-45-11 FAB (HEAVY CHAIN)
C: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)49,5483
Polymers49,5483
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-39 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 70.200, 118.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 95 / 2: CIS PROLINE - PRO L 141 / 3: CIS PROLINE - PRO H 160 / 4: CIS PROLINE - PRO H 162 / 5: CIS PROLINE - PRO H 202

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Components

#1: Antibody IGG1-KAPPA R45-45-11 FAB (LIGHT CHAIN)


Mass: 23549.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
#2: Antibody IGG1-KAPPA R45-45-11 FAB (HEAVY CHAIN)


Mass: 24777.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
#3: Protein/peptide CYCLOSPORIN A / Ciclosporin / CYCLOSPORINE / CICLOSPORIN / CICLOSPORINE / Ciclosporin


Type: Cyclic peptide / Class: ImmunosuppressantImmunosuppressive drug / Mass: 1220.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.22 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 14219 / Num. measured all: 63899 / Rmerge(I) obs: 0.087

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / Rfactor Rwork: 0.164 / Rfactor obs: 0.164
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 0 172 3651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 11236
Solvent computation
*PLUS
Displacement parameters
*PLUS

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