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- PDB-2yak: Structure of death-associated protein Kinase 1 (dapk1) in complex... -

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Basic information

Entry
Database: PDB / ID: 2yak
TitleStructure of death-associated protein Kinase 1 (dapk1) in complex with a ruthenium octasporine ligand (OSV)
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 1
KeywordsTRANSFERASE / OCTAHEDRAL RUTHENIUM INHIBITORY COMPLEX / KINASE INHIBITOR
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / protein autophosphorylation / regulation of apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / postsynaptic density / regulation of autophagy / negative regulation of translation / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / GTP binding / glutamatergic synapse / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RUTHENIUM OCTASPORINE 4 / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. ...Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, G. / Knapp, S. / Essen, L.-O. / Meggers, E.
Citation
Journal: J.Am.Chem.Soc. / Year: 2011
Title: Structurally Sophisticated Octahedral Metal Complexes as Highly Selective Protein Kinase Inhibitors.
Authors: Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, ...Authors: Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, G. / Knapp, S. / Essen, L.O. / Meggers, E.
#1: Journal: J.Am.Chem.Soc. / Year: 2008
Title: Targeting Large Kinase Active Site with Rigid, Bulky Octahedral Ruthenium Complexes.
Authors: Maksimoska, J. / Feng, L. / Harms, K. / Yi, C. / Kissil, J. / Marmorstein, R. / Meggers, E.
#2: Journal: Chembiochem / Year: 2008
Title: Extremely Tight Binding of a Ruthenium Complex to Glycogen Synthase Kinase 3.
Authors: Atilla-Gokcumen, G.E. / Pagano, N. / Streu, C. / Maksimoska, J. / Filippakopoulos, P. / Knapp, S. / Meggers, E.
History
DepositionFeb 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 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

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Assembly

Deposited unit
A: DEATH-ASSOCIATED PROTEIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4332
Polymers32,7251
Non-polymers7081
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.300, 77.800, 111.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DEATH-ASSOCIATED PROTEIN KINASE 1 / HUMAN DAPK1 / DAP KINASE 1


Mass: 32725.262 Da / Num. of mol.: 1 / Fragment: AA, RESIDUES 1-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET151 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-OSV / RUTHENIUM OCTASPORINE 4


Mass: 707.888 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31FN4O3RuS4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growDetails: 100 MM TRIS PH 7.2, 7.5-10% PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2010 / Details: PT COATED SI MIRRORS
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→24.53 Å / Num. obs: 21538 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.8 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE STRUCTURE OF DAPK1

Resolution: 2.2→24.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.548 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOPS AROUND ILE177 AND SER110 SHOW POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26043 1109 5.2 %RANDOM
Rwork0.19842 ---
obs0.20146 20406 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 40 108 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222326
X-RAY DIFFRACTIONr_bond_other_d0.0010.021590
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9913153
X-RAY DIFFRACTIONr_angle_other_deg0.993.0013876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59624.643112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44915410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2661513
X-RAY DIFFRACTIONr_chiral_restr0.1160.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
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_it1.0471.51385
X-RAY DIFFRACTIONr_mcbond_other0.2241.5558
X-RAY DIFFRACTIONr_mcangle_it1.93822241
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.833941
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.664.5911
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 78 -
Rwork0.32 1504 -
obs--96.35 %
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)
11.264-0.6276-0.31850.4932-0.30331.46250.0278-0.0638-0.08710.02860.04160.08130.02570.0874-0.06950.12130.00710.00450.10120.01340.0473-10.9035-22.561118.1223
20.2452-0.2595-0.05430.7798-0.04020.48290.04980.00510.02010.011-0.06850.0139-0.07690.00960.01860.0811-0.01510.00670.083-0.01350.0844-24.9033-4.62269.6531
39.8279-9.50460.588215.9873.02461.93570.6607-0.40690.478-0.9983-0.6927-0.5475-0.181-0.62370.0320.19220.03420.00210.2114-0.01170.0451-11.898-10.837816.892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 74
2X-RAY DIFFRACTION2A75 - 278
3X-RAY DIFFRACTION3A1279

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