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- PDB-5mag: Crystal structure of MELK in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 5mag
TitleCrystal structure of MELK in complex with an inhibitor
ComponentsMaternal embryonic leucine zipper kinase
KeywordsTRANSFERASE / kinase / inhibitor / complex
Function / homology
Function and homology information


neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / G2/M transition of mitotic cell cycle / histone H2AXY142 kinase activity / histone H3Y41 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / cell cortex ...neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / G2/M transition of mitotic cell cycle / histone H2AXY142 kinase activity / histone H3Y41 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / cell cortex / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / Rho-dependent protein serine/threonine kinase activity / ribosomal protein S6 kinase activity / histone H2BS14 kinase activity / histone H3T6 kinase activity / histone H3T45 kinase activity / histone H3S10 kinase activity / histone H3T11 kinase activity / AMP-activated protein kinase activity / protein autophosphorylation / cell population proliferation / histone H2AS1 kinase activity / non-specific serine/threonine protein kinase / positive regulation of apoptotic process / protein serine/threonine kinase activity / protein serine kinase activity / lipid binding / calcium ion binding / apoptotic process / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Maternal embryonic leucine zipper kinase, catalytic domain / : / Maternal embryonic leucine zipper kinase, UBA domain / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PF-3758309 / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCanevari, G. / Re Depaolini, S. / Casale, E. / Felder, E. / Kuster, B. / Heinzlmeir, S.
CitationJournal: Science / Year: 2017
Title: The target landscape of clinical kinase drugs.
Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / ...Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / Koch, H. / Schoof, M. / Canevari, G. / Casale, E. / Depaolini, S.R. / Feuchtinger, A. / Wu, Z. / Schmidt, T. / Rueckert, L. / Becker, W. / Huenges, J. / Garz, A.K. / Gohlke, B.O. / Zolg, D.P. / Kayser, G. / Vooder, T. / Preissner, R. / Hahne, H. / Tonisson, N. / Kramer, K. / Gotze, K. / Bassermann, F. / Schlegl, J. / Ehrlich, H.C. / Aiche, S. / Walch, A. / Greif, P.A. / Schneider, S. / Felder, E.R. / Ruland, J. / Medard, G. / Jeremias, I. / Spiekermann, K. / Kuster, B.
History
DepositionNov 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_contact_author / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8814
Polymers40,2211
Non-polymers6613
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint5 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.180, 62.810, 94.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maternal embryonic leucine zipper kinase / hMELK / Protein kinase Eg3 / pEg3 kinase / Protein kinase PK38 / hPK38 / Tyrosine-protein kinase MELK


Mass: 40220.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELK, KIAA0175 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-7KC / PF-3758309


Mass: 490.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30N8OS
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-20% PEG 3350 or PEG 4000, 0.1 M BIS TRIS pH 6.5, 0.6M NaCl
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2016 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.35→94.11 Å / Num. obs: 15037 / % possible obs: 95.9 % / Redundancy: 4.6 % / CC1/2: 0.981 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.7
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.9 / CC1/2: 0.885 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house MELK structure

Resolution: 2.35→52.24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / ESU R: 0.411 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25242 694 4.6 %RANDOM
Rwork0.19351 ---
obs0.19616 14303 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.056 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3---3.4 Å2
Refinement stepCycle: 1 / Resolution: 2.35→52.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 45 82 2692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192674
X-RAY DIFFRACTIONr_bond_other_d00.022614
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9923614
X-RAY DIFFRACTIONr_angle_other_deg3.5763.0036012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18924.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86515493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3291513
X-RAY DIFFRACTIONr_chiral_restr0.0790.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212907
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02601
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_it1.9233.4081253
X-RAY DIFFRACTIONr_mcbond_other1.9243.4051252
X-RAY DIFFRACTIONr_mcangle_it3.225.0771558
X-RAY DIFFRACTIONr_mcangle_other3.2195.0811559
X-RAY DIFFRACTIONr_scbond_it2.2653.7081421
X-RAY DIFFRACTIONr_scbond_other2.2643.7081421
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7885.4212056
X-RAY DIFFRACTIONr_long_range_B_refined5.76837.9512935
X-RAY DIFFRACTIONr_long_range_B_other5.76737.952935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 48 -
Rwork0.223 1088 -
obs--99.74 %

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