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- PDB-5n8v: Targeting the PEX14-PEX5 interaction by small molecules provides ... -

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Basic information

Entry
Database: PDB / ID: 5n8v
TitleTargeting the PEX14-PEX5 interaction by small molecules provides novel therapeutic routes to treat trypanosomiases.
ComponentsPeroxin 14
KeywordsSIGNALING PROTEIN / trypanosomiasis / glycosome / protein-protein interaction inhibitor / structure-based drug discovery / inhibitor
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-KZZ / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsDawidowski, M. / Emmanouilidis, L. / Sattler, M. / Popowicz, G.M.
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
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Peroxin 14
D: Peroxin 14
F: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,57120
Polymers31,5324
Non-polymers3,03816
Water4,179232
1
A: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8047
Polymers7,8831
Non-polymers9216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-26 kcal/mol
Surface area4230 Å2
MethodPISA
2
B: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6125
Polymers7,8831
Non-polymers7294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-32 kcal/mol
Surface area4140 Å2
MethodPISA
3
D: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6735
Polymers7,8831
Non-polymers7904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area4010 Å2
MethodPISA
4
F: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4813
Polymers7,8831
Non-polymers5982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-13 kcal/mol
Surface area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.760, 116.060, 38.820
Angle α, β, γ (deg.)90.00, 101.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABDF

#1: Protein
Peroxin 14


Mass: 7883.075 Da / Num. of mol.: 4 / Fragment: NP residues 20-84
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

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Non-polymers , 5 types, 248 molecules

#2: Chemical
ChemComp-KZZ / 1-(2-azanylethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-~{N}-(naphthalen-1-ylmethyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide


Mass: 519.637 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H33N5O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium Sulfate 0.1M Bis Tris Propane pH 7.5 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.549→37.99 Å / Num. obs: 44009 / % possible obs: 98.2 % / Redundancy: 3.3 % / CC1/2: 1 / Rmerge(I) obs: 0.029 / Net I/σ(I): 17.7
Reflection shellResolution: 1.549→1.576 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2174 / CC1/2: 0.902 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.754 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21748 2255 5.1 %RANDOM
Rwork0.19492 ---
obs0.19609 41737 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.055 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-1.45 Å2
2--1.99 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 204 232 2420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022232
X-RAY DIFFRACTIONr_bond_other_d0.0030.022159
X-RAY DIFFRACTIONr_angle_refined_deg1.2392.0963000
X-RAY DIFFRACTIONr_angle_other_deg0.923.0184977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3415254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52922.28983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87215414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5391524
X-RAY DIFFRACTIONr_chiral_restr0.0650.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212352
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02470
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_it0.9242.561010
X-RAY DIFFRACTIONr_mcbond_other0.9222.5591009
X-RAY DIFFRACTIONr_mcangle_it0.9123.8251257
X-RAY DIFFRACTIONr_mcangle_other0.9123.8271258
X-RAY DIFFRACTIONr_scbond_it1.3672.9141222
X-RAY DIFFRACTIONr_scbond_other1.3672.9141222
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.174.2341741
X-RAY DIFFRACTIONr_long_range_B_refined1.51531.2842765
X-RAY DIFFRACTIONr_long_range_B_other1.37330.5112696
X-RAY DIFFRACTIONr_rigid_bond_restr0.68434390
X-RAY DIFFRACTIONr_sphericity_free10.3695125
X-RAY DIFFRACTIONr_sphericity_bonded2.59454467
LS refinement shellResolution: 1.549→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 169 -
Rwork0.299 3011 -
obs--98.03 %

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