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- PDB-4ypd: Crystal Structure of DAPK1 catalytic domain in complex with the h... -

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Basic information

Entry
Database: PDB / ID: 4ypd
TitleCrystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE
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
4-methylpyridazine / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGrum-Tokars, V.L. / Minasov, G. / Roy, S.M. / Anderson, W.F. / Watterson, D.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)U01AG043415 United States
Citation
Journal: To Be Published
Title: Crystal Structure of DAPK1 catalytic domain in complex with hinge binding fragments
Authors: Grum-Tokars, V.L. / Minasov, G. / Roy, S.M. / Anderson, W.F. / Watterson, D.M.
#1: Journal: Plos One / Year: 2013
Title: Development of Novel In Vivo Chemical Probes to Address CNS Protein Kinase Involvement in Synaptic Dysfunction.
Authors: Watterson, D.M. / Grum-Tokars, V.L. / Roy, S.M. / Schavocky, J.P. / Bradaric, B.D. / Bachstetter, A.D. / Xing, B. / Dimayuga, E. / Saeed, F. / Zhang, H. / Staniszewski, A. / Pelletier, J.C. ...Authors: Watterson, D.M. / Grum-Tokars, V.L. / Roy, S.M. / Schavocky, J.P. / Bradaric, B.D. / Bachstetter, A.D. / Xing, B. / Dimayuga, E. / Saeed, F. / Zhang, H. / Staniszewski, A. / Pelletier, J.C. / Minasov, G. / Anderson, W.F. / Arancio, O. / Van Eldik, L.J.
#2: Journal: Biochim.Biophys.Acta / Year: 2011
Title: Site-directed mutagenesis of the glycine-rich loop of death associated protein kinase (DAPK) identifies it as a key structure for catalytic activity.
Authors: McNamara, L.K. / Brunzelle, J.S. / Schavocky, J.P. / Watterson, D.M. / Grum-Tokars, V.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0204
Polymers33,7941
Non-polymers2263
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-23 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.853, 62.511, 88.193
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 Death-associated protein kinase 1 / DAP kinase 1


Mass: 33794.367 Da / Num. of mol.: 1 / Fragment: protein kinase domain (UNP residues 2-285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Production host: Escherichia coli (E. coli)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DKG / 4-methylpyridazine


Mass: 94.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.91 Å3/Da / Density % sol: 35.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 1.7 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2011
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 57841 / % possible obs: 99.5 % / Redundancy: 7.2 % / Net I/σ(I): 23.33
Reflection shellHighest resolution: 1.35 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JKS

1jks


Resolution: 1.4→29.46 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.903 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1772 2610 5.1 %RANDOM
Rwork0.1551 ---
obs0.1562 48902 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.32 Å2 / Biso mean: 24.216 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.4→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 21 325 2629
Biso mean--32.83 34.57 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192655
X-RAY DIFFRACTIONr_bond_other_d0.0010.022538
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9773620
X-RAY DIFFRACTIONr_angle_other_deg0.77335894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2325340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54225.115131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1461514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.023089
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02601
X-RAY DIFFRACTIONr_mcbond_it1.4741.6341279
X-RAY DIFFRACTIONr_mcbond_other1.4721.6321278
X-RAY DIFFRACTIONr_mcangle_it2.2592.4461637
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 178 -
Rwork0.214 3581 -
all-3759 -
obs--100 %
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)
12.15521.25170.95991.90791.52371.82110.0871-0.0473-0.16510.1162-0.0459-0.19280.1682-0.0537-0.04120.06310.013-0.01430.01720.00770.066127.7385-2.96442.5052
20.7571-0.2202-0.31130.93550.75390.84690.0014-0.0164-0.0562-0.0034-0.036-0.00610.0981-0.02320.03460.0493-0.00170.00770.0357-0.0040.033219.50091.73124.1178
31.46280.0367-0.15891.21070.21621.01730.0176-0.09750.05130.04880.0405-0.1023-0.01740.1379-0.05810.0070.00090.00250.0405-0.01780.025716.748913.840314.2815
40.47570.16220.03220.9393-0.12860.87940.0237-0.0232-0.01970.02030.0157-0.01530.014-0.0264-0.03940.0038-0.00050.0010.00270.00070.01874.2610.52821.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 49
2X-RAY DIFFRACTION2A50 - 106
3X-RAY DIFFRACTION3A107 - 170
4X-RAY DIFFRACTION4A171 - 295

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