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- PDB-4zsd: Human Cyclophilin D Complexed with an Inhibitor at room temperature -

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Basic information

Entry
Database: PDB / ID: 4zsd
TitleHuman Cyclophilin D Complexed with an Inhibitor at room temperature
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / isomerase inhibitor complex
Function / homology
Function and homology information


: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation ...: / : / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / mitochondrial depolarization / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / necroptotic process / apoptotic mitochondrial changes / cellular response to calcium ion / response to ischemia / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to hydrogen peroxide / protein folding / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-7I6 / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsGelin, M. / Delfosse, V. / Allemand, F. / Hoh, F. / Sallaz-Damaz, Y. / Pirocchi, M. / Bourguet, W. / Ferrer, J.-L. / Labesse, G. / Guichou, J.-F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography.
Authors: Gelin, M. / Delfosse, V. / Allemand, F. / Hoh, F. / Sallaz-Damaz, Y. / Pirocchi, M. / Bourguet, W. / Ferrer, J.L. / Labesse, G. / Guichou, J.F.
History
DepositionMay 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1252
Polymers17,6521
Non-polymers4731
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.943, 57.943, 88.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / PPIase F / Cyclophilin D / CypD / Cyclophilin F / Mitochondrial cyclophilin / CyP-M / Rotamase F


Mass: 17652.125 Da / Num. of mol.: 1 / Fragment: UNP residues 44-207 / Mutation: K133I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase
#2: Chemical ChemComp-7I6 / 1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea


Mass: 472.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N4O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 30% PEG4000

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.45→57.94 Å / Num. obs: 25914 / % possible obs: 99.2 % / Redundancy: 2 % / Net I/σ(I): 7

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
Cootmodel building
RefinementResolution: 1.45→48.49 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.052 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1554 1335 4.9 %RANDOM
Rwork0.1338 ---
obs0.1349 25914 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 40.15 Å2 / Biso mean: 12.549 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å2-0 Å2
2--0.14 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.45→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 32 106 1361
Biso mean--19.66 25.51 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191321
X-RAY DIFFRACTIONr_bond_other_d0.0040.021254
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9741787
X-RAY DIFFRACTIONr_angle_other_deg1.3053.0092903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05124.80852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91715219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.913153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211501
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02304
X-RAY DIFFRACTIONr_mcbond_it0.7071.101664
X-RAY DIFFRACTIONr_mcbond_other0.7061.102665
X-RAY DIFFRACTIONr_mcangle_it0.8911.658828
X-RAY DIFFRACTIONr_rigid_bond_restr5.6532575
X-RAY DIFFRACTIONr_sphericity_free20.119544
X-RAY DIFFRACTIONr_sphericity_bonded3.30252604
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 92 -
Rwork0.205 1764 -
all-1856 -
obs--93.6 %

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