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- PDB-6ra1: Human Cyclophilin D in complex with norbornane fragment derivative -

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Basic information

Entry
Database: PDB / ID: 6ra1
TitleHuman Cyclophilin D in complex with norbornane fragment derivative
ComponentsPeptidyl-prolyl cis-trans isomerase F, mitochondrial
KeywordsISOMERASE / CYCLOPHILIN / BETA BARREL / PROLYL CIS/TRANS ISOMERASE / MITOC
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-JVQ / Chem-JWB / DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGraedler, U.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies.
Authors: Gradler, U. / Schwarz, D. / Blaesse, M. / Leuthner, B. / Johnson, T.L. / Bernard, F. / Jiang, X. / Marx, A. / Gilardone, M. / Lemoine, H. / Roche, D. / Jorand-Lebrun, C.
History
DepositionApr 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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)18,6167
Polymers17,6521
Non-polymers9646
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-20 kcal/mol
Surface area7460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.889, 56.889, 116.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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
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

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Non-polymers , 6 types, 85 molecules

#2: Chemical ChemComp-JWB / 2-[(1~{R},2~{R},6~{S},7~{S})-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]decan-4-yl]ethanoic acid


Mass: 223.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-JVQ / 14-ethyl-4,6-dioxa-10,14-diazatricyclo[7.6.0.0^{3,7}]pentadeca-1(9),2,7-trien-13-one


Mass: 248.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 50 mM potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→51.09 Å / Num. obs: 12987 / % possible obs: 95.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.48 Å2 / Rsym value: 0.113 / Net I/σ(I): 11.01
Reflection shellResolution: 2→2.25 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.04 / Num. unique obs: 3834 / Rsym value: 0.514 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J5B

4j5b


Resolution: 2→40.23 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1283 9.88 %RANDOM
Rwork0.192 ---
obs0.195 12985 95.8 %-
Displacement parametersBiso mean: 25.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.8231 Å20 Å20 Å2
2--2.8231 Å20 Å2
3----5.6463 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 64 79 1379
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111340HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.151806HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d474SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes223HARMONIC5
X-RAY DIFFRACTIONt_it1340HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion6.18
X-RAY DIFFRACTIONt_other_torsion13.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion167SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1607SEMIHARMONIC4
LS refinement shellResolution: 2→2.01 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2277 -10.38 %
Rwork0.1938 233 -
all0.1972 260 -
obs--98.16 %
Refinement TLS params.Method: refined / Origin x: -10.371 Å / Origin y: -8.76 Å / Origin z: -23.1023 Å
111213212223313233
T-0.0279 Å2-0.0041 Å20.0158 Å2--0.0728 Å2-0.0067 Å2---0.0397 Å2
L2.9982 °20.2474 °2-0.7705 °2-1.377 °2-0.2913 °2--1.2718 °2
S-0.0775 Å °0.3167 Å °-0.1298 Å °-0.0159 Å °0.0198 Å °0.022 Å °0.1319 Å °-0.1 Å °0.0578 Å °
Refinement TLS groupSelection details: { A|* }

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