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- PDB-5a6n: Crystal structure of human death associated protein kinase 3 (DAP... -

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Basic information

Entry
Database: PDB / ID: 5a6n
TitleCrystal structure of human death associated protein kinase 3 (DAPK3) in complex with compound 2
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 3
KeywordsTRANSFERASE / DAPK3 / HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 / DAP-LIKE KINASE / DLK / ZIPPER-INTERACTING PROTEIN KINASE / ZIP-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 focal adhesion assembly / regulation of mitotic nuclear division / chromosome, centromeric region / regulation of mitotic cell cycle ...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 focal adhesion assembly / regulation of mitotic nuclear division / chromosome, centromeric region / regulation of mitotic cell cycle / regulation of actin cytoskeleton organization / apoptotic signaling pathway / PML body / cellular response to type II interferon / small GTPase binding / spindle / positive regulation of canonical Wnt signaling pathway / regulation of cell shape / protein autophosphorylation / chromatin organization / midbody / regulation of apoptotic process / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / regulation of autophagy / intracellular signal transduction / cilium / positive regulation of cell migration / positive regulation of apoptotic process / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / centrosome / regulation of DNA-templated transcription / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DAPK3, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
S-1,2-PROPANEDIOL / 5-(3-SULFAMOYLPHENYL)-1H-1,2,3,4-TETRAZOL-1-IDE / Death-associated protein kinase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRodrigues, T. / Reker, D. / Welin, M. / Caldera, M. / Brunner, C. / Gabernet, G. / Schneider, P. / Walse, B. / Schneider, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: De Novo Fragment Design for Drug Discovery and Chemical Biology.
Authors: Rodrigues, T. / Reker, D. / Welin, M. / Caldera, M. / Brunner, C. / Gabernet, G. / Schneider, P. / Walse, B. / Schneider, G.
History
DepositionJun 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE 3
B: DEATH-ASSOCIATED PROTEIN KINASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6527
Polymers65,0902
Non-polymers5625
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-23 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.726, 87.775, 91.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998, 0.049, -0.043), (0.04, -0.043, -0.998), (-0.051, -0.988, 0.041)
Vector: 20.291, 251.393, 241.352)

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Components

#1: Protein DEATH-ASSOCIATED PROTEIN KINASE 3 / DAP KINASE 3 / DAP-LIKE KINASE / DLK / MYPT1 KINASE / ZIPPER-INTERACTING PROTEIN KINASE / ZIP-KINASE


Mass: 32545.123 Da / Num. of mol.: 2 / Fragment: PROTEIN KINASE DOMAIN, UNP RESIDUES 9-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O43293, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-U7E / 5-(3-SULFAMOYLPHENYL)-1H-1,2,3,4-TETRAZOL-1-IDE


Mass: 225.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N5O2S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 6.2
Details: 23% PROPANEDIOL, 0.1M NA/K PHOSPHATE PH 6.2, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2015
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→29.71 Å / Num. obs: 71490 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BHY

3bhy


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.875 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUE REFINED INDIVIDUALLY. RESIDUES 170-174 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21335 3449 4.8 %RANDOM
Rwork0.18268 ---
obs0.18416 67990 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4359 0 37 298 4694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194511
X-RAY DIFFRACTIONr_bond_other_d0.0020.024411
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.9756076
X-RAY DIFFRACTIONr_angle_other_deg1.153310173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33524.147217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27515854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0431532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.942.3482165
X-RAY DIFFRACTIONr_mcbond_other1.9352.3462164
X-RAY DIFFRACTIONr_mcangle_it2.9313.5112707
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8692.7852346
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 270 -
Rwork0.219 4886 -
obs--98.38 %

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