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- PDB-5l87: Targeting the PEX14-PEX5 interaction by small molecules provides ... -

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Basic information

Entry
Database: PDB / ID: 5l87
TitleTargeting the PEX14-PEX5 interaction by small molecules provides novel therapeutic routes to treat trypanosomiases.
ComponentsPeroxin 14
KeywordsMEMBRANE PROTEIN / trypanosomiasis / glycosome / protein-protein interaction inhibitor / structure-based drug discovery / inhibitor
Function / homology
Function and homology information


glycosome membrane / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression
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
Chem-6RD / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 Å
AuthorsDawidowski, M. / Emmanouilidis, L. / Sattler, M. / Popowicz, G.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR1905 ER178/4-1 Germany
CitationJournal: Science / Year: 2017
Title: Inhibitors of PEX14 disrupt protein import into glycosomes and kill Trypanosoma parasites.
Authors: Dawidowski, M. / Emmanouilidis, L. / Kalel, V.C. / Tripsianes, K. / Schorpp, K. / Hadian, K. / Kaiser, M. / Maser, P. / Kolonko, M. / Tanghe, S. / Rodriguez, A. / Schliebs, W. / Erdmann, R. ...Authors: Dawidowski, M. / Emmanouilidis, L. / Kalel, V.C. / Tripsianes, K. / Schorpp, K. / Hadian, K. / Kaiser, M. / Maser, P. / Kolonko, M. / Tanghe, S. / Rodriguez, A. / Schliebs, W. / Erdmann, R. / Sattler, M. / Popowicz, G.M.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / reflns_shell / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)8,3953
Polymers7,8831
Non-polymers5122
Water2,396133
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint1 kcal/mol
Surface area4060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.030, 37.260, 42.460
Angle α, β, γ (deg.)90.00, 117.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-257-

HOH

31A-300-

HOH

41A-333-

HOH

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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-6RD / 5-(1~{H}-indol-3-ylmethyl)-1-methyl-~{N}-(naphthalen-1-ylmethyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide


Mass: 449.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27N5O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 SPG Buffer pH 9.0 25% PEG 1500

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 0.86→90 Å / Num. obs: 203174 / % possible obs: 95.6 % / Redundancy: 4.2 % / Net I/σ(I): 18.23

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ff5

3ff5


Resolution: 0.87→37.53 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.367 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14538 2443 5.2 %RANDOM
Rwork0.12931 ---
obs0.13014 44871 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.02 Å2
2---0.02 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.87→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms485 0 38 133 656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02532
X-RAY DIFFRACTIONr_bond_other_d0.0090.02533
X-RAY DIFFRACTIONr_angle_refined_deg2.3912.078714
X-RAY DIFFRACTIONr_angle_other_deg1.0693.0181224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.98561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62522.63219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15515100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.743155
X-RAY DIFFRACTIONr_chiral_restr0.1030.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02118
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0960.735247
X-RAY DIFFRACTIONr_mcbond_other1.0960.73246
X-RAY DIFFRACTIONr_mcangle_it1.2521.1307
X-RAY DIFFRACTIONr_mcangle_other1.251.103308
X-RAY DIFFRACTIONr_scbond_it2.7460.968282
X-RAY DIFFRACTIONr_scbond_other2.7410.972283
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2131.378406
X-RAY DIFFRACTIONr_long_range_B_refined6.1489.51775
X-RAY DIFFRACTIONr_long_range_B_other6.1449.523776
X-RAY DIFFRACTIONr_rigid_bond_restr9.87931058
X-RAY DIFFRACTIONr_sphericity_free50.391520
X-RAY DIFFRACTIONr_sphericity_bonded12.12951169
LS refinement shellResolution: 0.87→0.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 122 -
Rwork0.309 2431 -
obs--70.25 %

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