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- PDB-5cen: Crystal structure of DLK (kinase domain) -

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Basic information

Entry
Database: PDB / ID: 5cen
TitleCrystal structure of DLK (kinase domain)
ComponentsMitogen-activated protein kinase kinase kinase 12
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / negative regulation of motor neuron apoptotic process / positive regulation of protein kinase activity / positive regulation of JUN kinase activity / JNK cascade / protein serine/threonine kinase activator activity / post-translational protein modification / growth cone / peptidyl-serine phosphorylation ...mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / negative regulation of motor neuron apoptotic process / positive regulation of protein kinase activity / positive regulation of JUN kinase activity / JNK cascade / protein serine/threonine kinase activator activity / post-translational protein modification / growth cone / peptidyl-serine phosphorylation / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase kinase kinase 12/13 / Mitogen-activated protein kinase kinase kinase 12 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Mitogen-activated protein kinase kinase kinase 12/13 / Mitogen-activated protein kinase kinase kinase 12 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsHARRIS, S.F. / YIN, J.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Scaffold-Hopping and Structure-Based Discovery of Potent, Selective, And Brain Penetrant N-(1H-Pyrazol-3-yl)pyridin-2-amine Inhibitors of Dual Leucine Zipper Kinase (DLK, MAP3K12).
Authors: Patel, S. / Harris, S.F. / Gibbons, P. / Deshmukh, G. / Gustafson, A. / Kellar, T. / Lin, H. / Liu, X. / Liu, Y. / Liu, Y. / Ma, C. / Scearce-Levie, K. / Ghosh, A.S. / Shin, Y.G. / Solanoy, ...Authors: Patel, S. / Harris, S.F. / Gibbons, P. / Deshmukh, G. / Gustafson, A. / Kellar, T. / Lin, H. / Liu, X. / Liu, Y. / Liu, Y. / Ma, C. / Scearce-Levie, K. / Ghosh, A.S. / Shin, Y.G. / Solanoy, H. / Wang, J. / Wang, B. / Yin, J. / Siu, M. / Lewcock, J.W.
History
DepositionJul 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 12


Theoretical massNumber of molelcules
Total (without water)34,0181
Polymers34,0181
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.289, 39.713, 59.907
Angle α, β, γ (deg.)90.000, 104.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 12 / Dual leucine zipper bearing kinase / DLK / Leucine-zipper protein kinase / ZPK / MAPK-upstream ...Dual leucine zipper bearing kinase / DLK / Leucine-zipper protein kinase / ZPK / MAPK-upstream kinase / MUK / Mixed lineage kinase


Mass: 34018.031 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 115-402)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K12, ZPK / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q12852, mitogen-activated protein kinase kinase kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 1.94 Å3/Da / Density % sol: 36.51 % / Mosaicity: 0.556 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.2 M magnesium acetate, 20% PEG 3350, 0.1 M HEPES pH 7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 5, 2010
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.7→75 Å / Num. obs: 29149 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 21.19 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.13 / Net I/av σ(I): 18.346 / Net I/σ(I): 9.2 / Num. measured all: 106694
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.763.60.62928810.952100
1.76-1.833.70.44428840.94100
1.83-1.913.70.3329010.957100
1.91-2.023.70.21228921.016100
2.02-2.143.70.15228991.111100
2.14-2.313.70.11429051.195100
2.31-2.543.70.10428881.431100
2.54-2.913.70.0829511.457100
2.91-3.663.60.04629220.88399.9
3.66-753.70.0430261.33299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNT2.9.1refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTC

3dtc


Resolution: 1.7→46.36 Å / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1467 5.06 %RANDOM
Rwork0.1851 ---
obs0.1871 29003 99.98 %-
Displacement parametersBiso max: 98.69 Å2 / Biso mean: 26.21 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1-4.5372 Å20 Å20.6646 Å2
2---2.6997 Å20 Å2
3----1.8376 Å2
Refine analyzeLuzzati coordinate error obs: 0.185 Å
Refinement stepCycle: final / Resolution: 1.7→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 0 209 2454
Biso mean---39.46 -
Num. residues----281
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d825SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes345HARMONIC5
X-RAY DIFFRACTIONt_it2368HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion301SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2980SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2368HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3225HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion17.32
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2154 132 4.69 %
Rwork0.2189 2685 -
all0.2188 2817 -
obs--99.98 %

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