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- PDB-5twy: Structure of Maternal Embryonic Leucine Zipper Kinase -

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Basic information

Entry
Database: PDB / ID: 5twy
TitleStructure of Maternal Embryonic Leucine Zipper Kinase
ComponentsMaternal embryonic leucine zipper kinaseMELK
KeywordsTransferase/Transferase Inhibitor / kinase / inhibitor / breast cancer / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase ...neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / lipid binding / calcium ion binding / 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
Chem-7LY / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.91 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
CitationJournal: Elife / Year: 2017
Title: MELK is not necessary for the proliferation of basal-like breast cancer cells.
Authors: Huang, H.T. / Seo, H.S. / Zhang, T. / Wang, Y. / Jiang, B. / Li, Q. / Buckley, D.L. / Nabet, B. / Roberts, J.M. / Paulk, J. / Dastjerdi, S. / Winter, G.E. / McLauchlan, H. / Moran, J. / ...Authors: Huang, H.T. / Seo, H.S. / Zhang, T. / Wang, Y. / Jiang, B. / Li, Q. / Buckley, D.L. / Nabet, B. / Roberts, J.M. / Paulk, J. / Dastjerdi, S. / Winter, G.E. / McLauchlan, H. / Moran, J. / Bradner, J.E. / Eck, M.J. / Dhe-Paganon, S. / Zhao, J.J. / Gray, N.S.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 6, 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

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Assembly

Deposited unit
A: Maternal embryonic leucine zipper kinase
B: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6404
Polymers78,7632
Non-polymers8772
Water0
1
A: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8202
Polymers39,3821
Non-polymers4391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8202
Polymers39,3821
Non-polymers4391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.860, 80.020, 79.800
Angle α, β, γ (deg.)90.000, 109.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 39381.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELK, KIAA0175 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-7LY / 2-(benzyloxy)-4-(1H-pyrazol-4-yl)-N-(2,3,4,5-tetrahydro-1H-3-benzazepin-7-yl)benzamide


Mass: 438.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H26N4O2

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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: 2.4 Å3/Da / Density % sol: 48.72 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.91→58.15 Å / Num. obs: 15793 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 88.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Net I/σ(I): 16.4 / Num. measured all: 53674
Reflection shellResolution: 2.91→2.99 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.614 / CC1/2: 0.847 / % possible all: 97

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→58.148 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.79
RfactorNum. reflection% reflection
Rfree0.3302 762 4.83 %
Rwork0.2861 --
obs0.2885 15765 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 282.75 Å2 / Biso mean: 107.7423 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.91→58.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4667 0 66 0 4733
Biso mean--84.73 --
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054845
X-RAY DIFFRACTIONf_angle_d0.8736593
X-RAY DIFFRACTIONf_chiral_restr0.046749
X-RAY DIFFRACTIONf_plane_restr0.006892
X-RAY DIFFRACTIONf_dihedral_angle_d3.5482907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9101-3.13480.49121320.42112980311297
3.1348-3.45020.36341410.36382970311197
3.4502-3.94940.3811420.33042992313497
3.9494-4.97540.34361750.26043006318198
4.9754-58.15940.27821720.24673055322797
Refinement TLS params.Method: refined / Origin x: 25.408 Å / Origin y: -20.8473 Å / Origin z: 17.8991 Å
111213212223313233
T0.3113 Å20.0204 Å20.0529 Å2-0.3409 Å20.1209 Å2--0.2147 Å2
L1.0375 °2-0.8856 °20.1333 °2-1.9526 °20.3632 °2--0.2886 °2
S-0.03 Å °0.1328 Å °-0.0665 Å °0.2398 Å °0.0334 Å °-0.1513 Å °0.0383 Å °0.2029 Å °0.0754 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 333
2X-RAY DIFFRACTION1allA4000
3X-RAY DIFFRACTION1allB0 - 4000

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