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- PDB-7qrc: X-ray structure of Trypanosoma cruzi PEX14 in complex with a PEX5... -

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Basic information

Entry
Database: PDB / ID: 7qrc
TitleX-ray structure of Trypanosoma cruzi PEX14 in complex with a PEX5-PEX14 PPI inhibitor
ComponentsPeroxin-14
KeywordsSIGNALING PROTEIN / Structure-based drug design / Inhibitor / Trypanosomiasis / Complex / PEX5-PEX14 PPI
Function / homology
Function and homology information


peroxisomal importomer complex / protein import into peroxisome matrix, docking / peroxisomal membrane / 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
Similarity search - Domain/homology
Chem-ET7 / Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsNapolitano, V. / Popowicz, G.M. / Dawidowski, M. / Dubin, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Accelerated Early staGe drug dIScovery (AEGIS)675555European Union
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Structure-based design, synthesis and evaluation of a novel family of PEX5-PEX14 interaction inhibitors against Trypanosoma.
Authors: Napolitano, V. / Mroz, P. / Marciniak, M. / Kalel, V.C. / Softley, C.A. / Janna Olmos, J.D. / Tippler, B.G. / Schorpp, K. / Rioton, S. / Frohlich, T. / Plettenburg, O. / Hadian, K. / ...Authors: Napolitano, V. / Mroz, P. / Marciniak, M. / Kalel, V.C. / Softley, C.A. / Janna Olmos, J.D. / Tippler, B.G. / Schorpp, K. / Rioton, S. / Frohlich, T. / Plettenburg, O. / Hadian, K. / Erdmann, R. / Sattler, M. / Popowicz, G.M. / Dawidowski, M. / Dubin, G.
History
DepositionJan 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Peroxin-14
A: Peroxin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9465
Polymers15,0412
Non-polymers9053
Water45025
1
B: Peroxin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0193
Polymers7,5211
Non-polymers4992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peroxin-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9272
Polymers7,5211
Non-polymers4061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.538, 25.416, 56.031
Angle α, β, γ (deg.)90.000, 105.560, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 59 / Label seq-ID: 3 - 60

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein Peroxin-14


Mass: 7520.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_80g13 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2V2WKZ5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ET7 / ~{N}-(5-ethyl-6-oxidanylidene-benzo[b][1,4]benzothiazepin-2-yl)-2-(4-fluorophenyl)ethanamide


Mass: 406.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H19FN2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.21 M MgCl2, 0.1 M Tris pH 8.5, 39% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.969 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: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.18→42.94 Å / Num. obs: 6430 / % possible obs: 98 % / Redundancy: 3.3 % / CC1/2: 0.98 / Net I/σ(I): 6.7
Reflection shellResolution: 2.18→2.24 Å / Num. unique obs: 527 / CC1/2: 0.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AON

5aon


Resolution: 2.18→42.94 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.872 / SU B: 16.857 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2844 313 4.9 %RANDOM
Rwork0.2711 ---
obs0.2717 6111 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.34 Å2 / Biso mean: 39.349 Å2 / Biso min: 20.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å20 Å20.08 Å2
2---2.39 Å20 Å2
3----0.83 Å2
Refinement stepCycle: final / Resolution: 2.18→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 64 25 978
Biso mean--31.62 34.31 -
Num. residues----120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131003
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.7341361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5425128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54123.17141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38615167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.819155
X-RAY DIFFRACTIONr_chiral_restr0.0660.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02768
Refine LS restraints NCS

Ens-ID: 1 / Number: 1668 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.18→2.234 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.29 23 -
Rwork-435 -
obs--94.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.7392-0.7777-3.59599.2249-0.01696.13560.0981-0.11120.22660.187-0.04620.85060.1441-0.6857-0.05190.0135-0.03940.02160.2738-0.00740.1658-6.31112.047411.9435
28.64941.94472.73848.33221.09195.04430.0789-0.1759-0.2210.2392-0.0285-0.7041-0.22680.4057-0.05040.0254-0.0186-0.01620.23890.0110.142613.32750.61412.258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 201
2X-RAY DIFFRACTION2A2 - 102

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