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- PDB-3rdc: Human Cyclophilin D Complexed with an Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3rdc
TitleHuman Cyclophilin D Complexed with an Inhibitor
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 / 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
ethyl N-[(4-aminobenzyl)carbamoyl]glycinate / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsColliandre, L. / Ahmed-Belkacem, H. / Bessin, Y. / Pawlotsky, J.M. / Guichou, J.F.
Citation
Journal: 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.
#1: Journal: 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
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,1222
Polymers17,8701
Non-polymers2511
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.445, 56.445, 86.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 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-EA4 / ethyl N-[(4-aminobenzyl)carbamoyl]glycinate


Mass: 251.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.94 Å3/Da / Density % sol: 36.56 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 12, 2008
RadiationMonochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→28.2 Å / Num. all: 10623 / Num. obs: 10358 / % possible obs: 97.5 % / Observed criterion σ(I): 9.1 / Redundancy: 4.1 % / Rsym value: 0.059
Reflection shellResolution: 1.93→1.987 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.188 / % possible all: 84

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
X-PLORmodel building
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BIT

2bit


Resolution: 1.94→25.79 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.853 / SU B: 4.259 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27014 529 4.9 %RANDOM
Rwork0.20461 ---
obs0.20781 10358 98.99 %-
all-10623 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.94→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 18 223 1473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221277
X-RAY DIFFRACTIONr_bond_other_d0.0020.02865
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9621721
X-RAY DIFFRACTIONr_angle_other_deg0.8093.0032102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29224.5151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.36215208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.106154
X-RAY DIFFRACTIONr_chiral_restr0.0630.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211439
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_mcbond_it0.3491.5810
X-RAY DIFFRACTIONr_mcbond_other0.0841.5345
X-RAY DIFFRACTIONr_mcangle_it0.60521301
X-RAY DIFFRACTIONr_scbond_it0.973467
X-RAY DIFFRACTIONr_scangle_it1.4774.5420
LS refinement shellResolution: 1.937→1.987 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 37 -
Rwork0.186 672 -
obs--90.66 %

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