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- PDB-3bqr: Crystal structure of human death associated protein kinase 3 (DAP... -

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Basic information

Entry
Database: PDB / ID: 3bqr
TitleCrystal structure of human death associated protein kinase 3 (DAPK3) in complex with an imidazo-pyridazine ligand
ComponentsDeath-associated protein kinase 3
KeywordsTRANSFERASE / Death Associated Kinase / DAPK3 / ZIP kinase / ZIPK / DAP kinase 3 / DAP like kinase / Dlk / Structural Genomics Consortium / SGC / Apoptosis / ATP-binding / Chromatin regulator / Nucleotide-binding / Nucleus / Serine/threonine-protein kinase
Function / homology
Function and homology information


regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / regulation of cell motility / Caspase activation via Dependence Receptors in the absence of ligand / regulation of mitotic nuclear division / regulation of focal adhesion assembly / regulation of mitotic cell cycle / regulation of autophagy ...regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / regulation of cell motility / Caspase activation via Dependence Receptors in the absence of ligand / regulation of mitotic nuclear division / regulation of focal adhesion assembly / regulation of mitotic cell cycle / regulation of autophagy / apoptotic signaling pathway / regulation of actin cytoskeleton organization / PML body / small GTPase binding / cellular response to type II interferon / positive regulation of canonical Wnt signaling pathway / chromatin organization / regulation of cell shape / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of cell migration / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DAPK3, 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. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...DAPK3, 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. / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4RB / S-1,2-PROPANEDIOL / Death-associated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsFilippakopoulos, P. / Rellos, P. / Fedorov, O. / Niesen, F. / Pike, A.C.W. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Rellos, P. / Fedorov, O. / Niesen, F. / Pike, A.C.W. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Death Associated Protein Kinase 3 (DAPK3) in Complex with an Imidazo-Pyridazine Ligand.
Authors: Filippakopoulos, P. / Rellos, P. / Fedorov, O. / Niesen, F. / Pike, A.C.W. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Knapp, S.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1165
Polymers32,5451
Non-polymers5714
Water5,477304
1
A: Death-associated protein kinase 3
hetero molecules

A: Death-associated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23210
Polymers65,0902
Non-polymers1,1418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.533, 83.533, 113.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Death-associated protein kinase 3 / DAP kinase 3 / DAP-like kinase / Dlk / ZIP-kinase


Mass: 32545.123 Da / Num. of mol.: 1 / Fragment: Protein kinase domain: Residues 9-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK3, ZIPK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(R3)
References: UniProt: O43293, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4RB / 4-(6-{[(1R)-1-(hydroxymethyl)propyl]amino}imidazo[1,2-b]pyridazin-3-yl)benzoic acid


Mass: 326.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O3
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25% 1,2-propanediol, 10% Glycerol, 0.1M Na/K phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98248 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98248 Å / Relative weight: 1
ReflectionRedundancy: 8.5 % / Av σ(I) over netI: 15.1 / Number: 330854 / Rmerge(I) obs: 0.061 / Χ2: 1.02 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 39150 / % possible obs: 94.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.775097.310.0321.0178.6
2.993.7790.910.0571.0228.7
2.612.9910010.0511.0259.7
2.382.6110010.0711.0029.6
2.22.3876.310.1081.0177.6
2.072.210010.1521.0289.1
1.972.0710010.2261.038.9
1.891.9784.710.4221.0095.8
1.811.8999.810.661.0428.5
1.751.8198.910.8941.0257.4
ReflectionResolution: 1.75→50 Å / Num. all: 41297 / Num. obs: 39150 / % possible obs: 94.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 1.022 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 2.22 / Num. unique all: 3999 / Rsym value: 0.894 / Χ2: 1.025 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.49 Å
Translation1.75 Å35.49 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YRP

1yrp


Resolution: 1.75→35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.2 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1965 5 %RANDOM
Rwork0.18 ---
all0.181 39058 --
obs0.181 39058 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 40 304 2526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222305
X-RAY DIFFRACTIONr_bond_other_d0.0010.021611
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9823102
X-RAY DIFFRACTIONr_angle_other_deg1.4213.0013911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.745273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37923.853109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41915429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8831518
X-RAY DIFFRACTIONr_chiral_restr0.1120.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
X-RAY DIFFRACTIONr_mcbond_it3.06431372
X-RAY DIFFRACTIONr_mcbond_other1.0083556
X-RAY DIFFRACTIONr_mcangle_it4.45452227
X-RAY DIFFRACTIONr_scbond_it7.3578933
X-RAY DIFFRACTIONr_scangle_it9.70511874
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 146 -
Rwork0.247 2778 -
all-2924 -
obs--97.86 %
Refinement TLS params.Method: refined / Origin x: 13.7805 Å / Origin y: 42.2295 Å / Origin z: 28.5283 Å
111213212223313233
T-0.0297 Å20.0104 Å2-0.0115 Å2--0.0882 Å20.0152 Å2---0.0832 Å2
L0.9252 °2-0.0084 °2-0.1964 °2-0.5211 °20.0258 °2--0.5451 °2
S-0.0316 Å °-0.0138 Å °0.0342 Å °-0.049 Å °0.0104 Å °0.005 Å °0.0267 Å °-0.0193 Å °0.0212 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1721 - 166
2X-RAY DIFFRACTION1AA176 - 191170 - 185
3X-RAY DIFFRACTION1AA192 - 284186 - 278
4X-RAY DIFFRACTION1AB4011

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