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- PDB-6r9x: Human Cyclophilin D in complex with N-cyclopentyl-N'-pyridin-2-yl... -

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Basic information

Entry
Database: PDB / ID: 6r9x
TitleHuman Cyclophilin D in complex with N-cyclopentyl-N'-pyridin-2-ylmethyl-oxalamide
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-JW2 / Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 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 4, 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)17,8992
Polymers17,6521
Non-polymers2471
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.239, 57.239, 87.603
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-732-

HOH

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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: 44-207 (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-JW2 / ~{N}'-cyclopentyl-~{N}-(pyridin-2-ylmethyl)ethanediamide


Mass: 247.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsALIGNMENT: - Global alignment of extracted AA sequence from the pdb file with the original sequence ...ALIGNMENT: - Global alignment of extracted AA sequence from the pdb file with the original sequence inserted in the template - Be aware that the alignment is the best one for the given scoring schemata but does not have to be the best one out of all kinds of possible alignments! - No substitution matrix used. Just matches, mismatches and gaps ar considered - The first sequence was extracted from the xml-template file according to the chosen template. The second sequence was extract from the ATOM section of the pdb file. GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGD GNPLVYLDVDANGKPLGR-VLELKAD-VPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGD FTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGH FTNHNGT-GKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQ-FICTIKTDWLDGKH-VFGH VIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS VIEGMD-V-KIESFGSKSGRTS-KIVITDCGQLS

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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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.66→87.6 Å / Num. obs: 16838 / % possible obs: 94.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 11.14 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.51
Reflection shellResolution: 1.66→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.195 / Num. unique obs: 5436 / % possible all: 91.4

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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: 1.66→15.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1695 10.09 %RANDOM
Rwork0.144 ---
obs0.149 16793 94.9 %-
Displacement parametersBiso mean: 10.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.372 Å20 Å20 Å2
2--0.372 Å20 Å2
3----0.744 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.66→15.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 18 333 1589
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011298HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.041749HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d449SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes222HARMONIC5
X-RAY DIFFRACTIONt_it1298HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.27
X-RAY DIFFRACTIONt_other_torsion13.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion162SEMIHARMONIC5
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_contact1828SEMIHARMONIC4
LS refinement shellResolution: 1.66→1.68 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3563 -8.04 %
Rwork0.2918 309 -
all0.2968 336 -
obs--77.31 %
Refinement TLS params.Method: refined / Origin x: 12.2253 Å / Origin y: 14.0753 Å / Origin z: 23.6711 Å
111213212223313233
T-0.0668 Å20.0016 Å2-0.0014 Å2--0.0622 Å20.005 Å2---0.0662 Å2
L0.0961 °20.0478 °2-0.039 °2-0.2409 °20.0258 °2--0.3613 °2
S0.0059 Å °0.0109 Å °-0.0037 Å °-0.0476 Å °0.0049 Å °-0.0098 Å °0.0356 Å °0.001 Å °-0.0107 Å °
Refinement TLS groupSelection details: { A|* }

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