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- PDB-6spt: High resolution crystal structure of N-terminal domain of PEX14 f... -

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Basic information

Entry
Database: PDB / ID: 6spt
TitleHigh resolution crystal structure of N-terminal domain of PEX14 from Trypanosoma brucei in complex with the fist compound with sub-micromolar trypanocidal activity
ComponentsPeroxin 14
KeywordsSIGNALING PROTEIN / PEX5-PEX14 protein protein inhibitor / HAT / peroxisome / Trypanosoma
Function / homology
Function and homology information


glycosome membrane / peroxisomal importomer complex / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression / signaling receptor binding
Similarity search - Function
Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-FTW / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsNapolitano, V. / Dawidowski, M. / Kalel, V.C. / Fino, R. / Emmanouilidis, L. / Lenhart, D. / Ostertag, M. / Kaiser, M. / Kolonko, M. / Schilebs, W. ...Napolitano, V. / Dawidowski, M. / Kalel, V.C. / Fino, R. / Emmanouilidis, L. / Lenhart, D. / Ostertag, M. / Kaiser, M. / Kolonko, M. / Schilebs, W. / Maser, P. / Tetko, I. / Hadian, K. / Plettenburg, O. / Erdmann, R. / Sattler, M. / Popowicz, G.M. / Dubin, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Accelerated Early staGe drug dIScovery675555 Germany
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structure-Activity Relationship in Pyrazolo[4,3-c]pyridines, First Inhibitors of PEX14-PEX5 Protein-Protein Interaction with Trypanocidal Activity.
Authors: Dawidowski, M. / Kalel, V.C. / Napolitano, V. / Fino, R. / Schorpp, K. / Emmanouilidis, L. / Lenhart, D. / Ostertag, M. / Kaiser, M. / Kolonko, M. / Tippler, B. / Schliebs, W. / Dubin, G. / ...Authors: Dawidowski, M. / Kalel, V.C. / Napolitano, V. / Fino, R. / Schorpp, K. / Emmanouilidis, L. / Lenhart, D. / Ostertag, M. / Kaiser, M. / Kolonko, M. / Tippler, B. / Schliebs, W. / Dubin, G. / Maser, P. / Tetko, I.V. / Hadian, K. / Plettenburg, O. / Erdmann, R. / Sattler, M. / Popowicz, G.M.
History
DepositionSep 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8519
Polymers7,8831
Non-polymers9688
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-31 kcal/mol
Surface area4750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.935, 45.935, 63.733
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Peroxin 14


Mass: 7883.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PEX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IEW2
#2: Chemical ChemComp-FTW / 5-[(4-methoxynaphthalen-1-yl)methyl]-1-[2-[(2-methyl-1-oxidanyl-propan-2-yl)amino]ethyl]-~{N}-(naphthalen-1-ylmethyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide


Mass: 591.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H41N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 0.1 M Tris pH 8, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.2→39.78 Å / Num. obs: 23334 / % possible obs: 93.7 % / Redundancy: 3.93 % / Biso Wilson estimate: 15.045 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.082 / Χ2: 0.948 / Net I/σ(I): 9.42 / Num. measured all: 91713
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.33.3670.2912.9715149521544990.890.34586.3
1.3-1.53.9740.2114.9225853675865060.950.24296.3
1.5-24.0620.10110.0528739736570750.9890.11696.1
2-2.54.2580.0617.7610751264625250.9940.06895.4
2.5-34.160.05419.974597119111050.9950.06292.8
3-54.190.05322.745304132312660.9960.06195.7
5-103.7880.06621.2911593463060.9940.07788.4
10-203.2170.06721.0614851460.9980.08190.2
20-39.782.1670.03417.59138610.0475

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→39.78 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.131 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1524 1155 4.9 %RANDOM
Rwork0.1084 ---
obs0.1106 22179 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.79 Å2 / Biso mean: 13.924 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.2→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms552 0 68 136 756
Biso mean--17.13 26.68 -
Num. residues----69
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.019769
X-RAY DIFFRACTIONr_bond_other_d0.0020.019763
X-RAY DIFFRACTIONr_angle_refined_deg2.671.9451047
X-RAY DIFFRACTIONr_angle_other_deg1.2893.0011781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.628598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45823.63633
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10415154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.064157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021026
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02171
X-RAY DIFFRACTIONr_rigid_bond_restr6.46531530
X-RAY DIFFRACTIONr_sphericity_free28.747531
X-RAY DIFFRACTIONr_sphericity_bonded12.17151611
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 74 -
Rwork0.194 1275 -
all-1349 -
obs--74.45 %

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