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- PDB-5l8a: Targeting the PEX14-PEX5 interaction by small molecules provides ... -

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Basic information

Entry
Database: PDB / ID: 5l8a
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 / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / posttranscriptional 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-6RB / GLYCINE / Peroxin-14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references

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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
C: Peroxin 14
D: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,57511
Polymers31,5324
Non-polymers2,0427
Water4,972276
1
A: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4293
Polymers7,8831
Non-polymers5462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3542
Polymers7,8831
Non-polymers4711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3773
Polymers7,8831
Non-polymers4942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peroxin 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4163
Polymers7,8831
Non-polymers5332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)36.100, 36.280, 55.310
Angle α, β, γ (deg.)94.12, 105.87, 100.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 66
2010B5 - 66
1020A5 - 66
2020C5 - 66
1030A5 - 66
2030D5 - 66
1040B5 - 66
2040C5 - 66
1050B5 - 66
2050D5 - 66
1060C5 - 66
2060D5 - 66

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Peroxin 14 /


Mass: 7883.075 Da / Num. of mol.: 4
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, 283 molecules

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


Mass: 470.563 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H30N4O3
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG Buffer pH6 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.57→31.3 Å / Num. obs: 33844 / % possible obs: 92.7 % / Redundancy: 3.6 % / Net I/σ(I): 7.5
Reflection shellResolution: 1.57→1.66 Å / Rmerge(I) obs: 0.603

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FF5
Resolution: 1.57→27.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.226 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25171 1687 5 %RANDOM
Rwork0.1908 ---
obs0.19388 32107 92.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0.19 Å20.17 Å2
2---0.95 Å20.24 Å2
3---1.54 Å2
Refinement stepCycle: 1 / Resolution: 1.57→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 150 276 2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022127
X-RAY DIFFRACTIONr_bond_other_d0.0110.022116
X-RAY DIFFRACTIONr_angle_refined_deg2.2442.0732851
X-RAY DIFFRACTIONr_angle_other_deg1.9583.024871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3765244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00122.30878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78815398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2281522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212270
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02472
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_it2.6841.6991
X-RAY DIFFRACTIONr_mcbond_other2.6351.596987
X-RAY DIFFRACTIONr_mcangle_it2.6932.391230
X-RAY DIFFRACTIONr_mcangle_other2.6652.391229
X-RAY DIFFRACTIONr_scbond_it3.5351.9811136
X-RAY DIFFRACTIONr_scbond_other3.5351.9811136
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5782.8231622
X-RAY DIFFRACTIONr_long_range_B_refined4.1414.6312743
X-RAY DIFFRACTIONr_long_range_B_other4.11314.6262743
X-RAY DIFFRACTIONr_rigid_bond_restr5.25334243
X-RAY DIFFRACTIONr_sphericity_free22.1185117
X-RAY DIFFRACTIONr_sphericity_bonded7.31554369
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A38020.07
12B38020.07
21A37970.09
22C37970.09
31A38870.08
32D38870.08
41B37940.08
42C37940.08
51B37410.08
52D37410.08
61C37750.1
62D37750.1
LS refinement shellResolution: 1.573→1.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 119 -
Rwork0.221 2065 -
obs--83.3 %

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