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- PDB-6vxr: Structure of Maternal embryonic leucine zipper kinase bound to LDSM276 -

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Basic information

Entry
Database: PDB / ID: 6vxr
TitleStructure of Maternal embryonic leucine zipper kinase bound to LDSM276
ComponentsMaternal embryonic leucine zipper kinaseMELK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein kinase / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE / 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 / 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-F7D / Maternal embryonic leucine zipper kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCounago, R.M. / Takarada, J.E. / dos Reis, C.V. / Gama, F.H. / Azevedo, H. / Mascarello, A. / Guimaraes, C.R. / Structural Genomics Consortium (SGC)
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/50724-5 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)465651/2014-3 Brazil
Sao Paulo Research Foundation (FAPESP)2014/50897-0 Brazil
CitationJournal: To Be Published
Title: Structure of Maternal embryonic leucine zipper kinase bound to LDSM276
Authors: Counago, R.M. / Takarada, J.E. / dos Reis, C.V. / Guimaraes, C.R. / Azevedo, H. / Mascarello, A. / Gama, F.H.
History
DepositionFeb 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Maternal embryonic leucine zipper kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7413
Polymers39,2961
Non-polymers4452
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.124, 70.159, 102.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 39295.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELK, KIAA0175 / Plasmid: pNIC-ZB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): R3
References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-F7D / (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one


Mass: 383.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1,500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2→19.85 Å / Num. obs: 25981 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.028 / Rrim(I) all: 0.099 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0513.22.6792467818710.5060.7642.7881.1100
8.94-19.8410.40.0632233110.9980.0190.06341.991.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IH9

5ih9


Resolution: 2.1→19.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.757 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.182
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1128 5 %RANDOM
Rwork0.219 ---
obs0.2206 21334 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.73 Å2 / Biso mean: 51.597 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2---0.82 Å20 Å2
3----1.91 Å2
Refinement stepCycle: final / Resolution: 2.1→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 32 47 2509
Biso mean--49.81 53.76 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132525
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172297
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.6343432
X-RAY DIFFRACTIONr_angle_other_deg1.1731.5715309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56623.305118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89115418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.194159
X-RAY DIFFRACTIONr_chiral_restr0.0490.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 72 -
Rwork0.289 1526 -
all-1598 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 24.2533 Å / Origin y: 3.9553 Å / Origin z: 9.4541 Å
111213212223313233
T0.0705 Å2-0.0596 Å2-0.0208 Å2-0.0844 Å20.0053 Å2--0.0208 Å2
L2.0878 °2-0.6967 °2-1.1386 °2-1.63 °20.5922 °2--3.5573 °2
S-0.0293 Å °0.2082 Å °-0.1626 Å °0.1183 Å °-0.0155 Å °0.0443 Å °0.1389 Å °-0.1408 Å °0.0448 Å °

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