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- PDB-6gvx: Crystal structure of Maternal Embryonic Leucine Zipper Kinase (ME... -

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Basic information

Entry
Database: PDB / ID: 6gvx
TitleCrystal structure of Maternal Embryonic Leucine Zipper Kinase (MELK) in complex with dorsomorphin (Compound C)
ComponentsMaternal embryonic leucine zipper kinase
KeywordsONCOPROTEIN / dorsomorphin / MELK / inhibitor / cancer
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 / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / apoptotic process / 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-TAK / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsGolik, P. / Rembacz, K.P. / Zrubek, K. / Romanowska, M. / Bugusz, J. / Wladyka, B. / Dubin, G.
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: Crystal structure of Maternal Embryonic Leucine Zipper Kinase (MELK) in complex with dorsomorphin (Compound C).
Authors: Rembacz, K.P. / Zrubek, K.M. / Golik, P. / Michalik, K. / Bogusz, J. / Wladyka, B. / Romanowska, M. / Dubin, G.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Maternal embryonic leucine zipper kinase
B: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3696
Polymers79,4462
Non-polymers9234
Water2,396133
1
A: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1853
Polymers39,7231
Non-polymers4622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1853
Polymers39,7231
Non-polymers4622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.475, 80.074, 77.975
Angle α, β, γ (deg.)90.00, 110.58, 90.00
Int Tables number4
Space group name H-MP1211

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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: 39723.098 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)
References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-TAK / 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine / Dorsomorphin


Mass: 399.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.24→48.672 Å / Num. obs: 36063 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.75 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.7
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.8 / Num. unique obs: 3575 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2V

4d2v


Resolution: 2.24→48.672 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1777 4.93 %
Rwork0.2032 --
obs0.205 36033 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→48.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 68 133 5085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025086
X-RAY DIFFRACTIONf_angle_d0.5696906
X-RAY DIFFRACTIONf_dihedral_angle_d9.6241803
X-RAY DIFFRACTIONf_chiral_restr0.021777
X-RAY DIFFRACTIONf_plane_restr0.002864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30060.3221200.3092517X-RAY DIFFRACTION94
2.3006-2.36830.30911470.25642628X-RAY DIFFRACTION100
2.3683-2.44470.29291540.24692631X-RAY DIFFRACTION100
2.4447-2.53210.291400.23372634X-RAY DIFFRACTION100
2.5321-2.63350.26481250.2392638X-RAY DIFFRACTION100
2.6335-2.75330.25861400.24142616X-RAY DIFFRACTION98
2.7533-2.89840.27011480.22262616X-RAY DIFFRACTION100
2.8984-3.080.25011500.22472657X-RAY DIFFRACTION100
3.08-3.31780.26611330.21732665X-RAY DIFFRACTION100
3.3178-3.65150.24081390.20462620X-RAY DIFFRACTION98
3.6515-4.17970.21831270.17252636X-RAY DIFFRACTION99
4.1797-5.2650.2041120.16272697X-RAY DIFFRACTION100
5.265-48.68320.20791420.19662701X-RAY DIFFRACTION99
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)
15.824-3.0685-4.16349.2625.58927.74390.0181-0.1310.1065-0.52730.48380.2657-0.1011-0.9063-0.46920.47170.0033-0.00960.93180.27020.3594-8.2002-13.3456-6.6468
24.68310.42292.45820.4232-0.85967.0715-0.1199-0.00120.0812-0.09880.2390.03760.2952-0.9307-0.10960.3471-0.01950.06150.33580.07070.35291.1937-15.1768.4939
36.0508-1.6326-0.07034.6171-0.26693.93290.157-0.2313-0.1444-0.0983-0.0623-0.25690.7062-0.4693-0.03620.4337-0.0795-0.04120.27630.04510.26617.2023-21.121112.6267
43.07590.17011.58530.8281-1.14624.96070.0671-0.51960.03490.25490.09730.1270.1241-0.8495-0.07160.26020.00340.10670.3702-0.00230.29585.1527-14.828618.3019
52.68030.5193-3.3058.4788-5.91988.98770.3507-0.2342-0.18840.5889-0.37760.22620.30240.59330.02470.6936-0.224-0.10320.55140.02440.347819.8534-11.2402-1.7892
63.96030.50811.16990.78390.02095.13890.106-0.4417-0.30290.1613-0.22470.06690.28330.04670.12460.4183-0.09240.03480.24010.01070.39313.9798-11.3507-14.0954
77.6156-0.38460.59131.3266-1.04635.3816-0.02660.0211-0.0274-0.0790.0728-0.07390.2234-0.1845-0.03130.3724-0.0746-0.03390.1806-0.03530.26495.1608-9.3714-26.0427
83.39130.27561.44070.76350.11573.78490.23430.2417-0.2722-0.19890.00950.0730.9001-0.5993-0.11980.645-0.2062-0.06520.39530.00130.3695-1.3747-15.9451-31.3146
96.03371.83421.69088.1517-0.23793.08910.27740.22010.2183-0.0598-0.5258-0.538-0.47311.06560.1930.4198-0.17760.01370.61370.07810.356530.00221.0535-18.7022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 187 )
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 333 )
5X-RAY DIFFRACTION5chain 'B' and (resid -3 through 23 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 105 )
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 148 )
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 283 )
9X-RAY DIFFRACTION9chain 'B' and (resid 284 through 335 )

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