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- PDB-3r56: Human Cyclophilin D Complexed with a Fragment -

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Basic information

Entry
Database: PDB / ID: 3r56
TitleHuman Cyclophilin D Complexed with a Fragment
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE/ISOMERASE INHIBITOR / beta barrel / prolyl cis/trans isomerase / mitochondria / inhibitor / ISOMERASE-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 / apoptotic mitochondrial changes / necroptotic process / 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
1H-indazol-6-amine / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsColliandre, L. / Ahmed-Belkacem, H. / Bessin, Y. / Pawlotsky, J.M. / Guichou, J.F.
CitationJournal: Nat Commun / Year: 2016
Title: Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.
Authors: Ahmed-Belkacem, A. / Colliandre, L. / Ahnou, N. / Nevers, Q. / Gelin, M. / Bessin, Y. / Brillet, R. / Cala, O. / Douguet, D. / Bourguet, W. / Krimm, I. / Pawlotsky, J.M. / Guichou, J.F.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,3303
Polymers17,8701
Non-polymers4602
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.030, 57.030, 86.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase F, mitochondrial / Cyclophilin F / PPIase F / Rotamase F


Mass: 17870.400 Da / Num. of mol.: 1 / Fragment: UNP residues 43-207 / Mutation: K175I
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-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical ChemComp-6AI / 1H-indazol-6-amine


Mass: 133.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 30% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97968
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2008
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97968 Å / Relative weight: 1
ReflectionResolution: 1.4→25.51 Å / Num. all: 25100 / Num. obs: 23793 / % possible obs: 87.8 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 16.5 / Redundancy: 4.8 % / Rsym value: 0.042
Reflection shellResolution: 1.4→1.436 Å / Redundancy: 3.8 % / Rsym value: 0.252 / % possible all: 78

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Processing

Software
NameVersionClassification
DNAdata collection
X-PLORmodel building
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→25.51 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.915 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18727 1290 5.1 %RANDOM
Rwork0.15777 ---
obs0.15926 23793 86.58 %-
all-25100 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.4→25.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 32 321 1593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221314
X-RAY DIFFRACTIONr_bond_other_d0.0030.02917
X-RAY DIFFRACTIONr_angle_refined_deg0.9851.9711764
X-RAY DIFFRACTIONr_angle_other_deg0.8193.0022235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84824.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.46715219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.166156
X-RAY DIFFRACTIONr_chiral_restr0.0630.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02266
X-RAY DIFFRACTIONr_mcbond_it0.271.5809
X-RAY DIFFRACTIONr_mcbond_other0.0531.5343
X-RAY DIFFRACTIONr_mcangle_it0.50221302
X-RAY DIFFRACTIONr_scbond_it0.6733505
X-RAY DIFFRACTIONr_scangle_it1.0774.5461
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 82 -
Rwork0.226 1439 -
obs--73.41 %

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