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- PDB-7ccu: Crystal structure of death-associated protein kinase 1 in complex... -

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Basic information

Entry
Database: PDB / ID: 7ccu
TitleCrystal structure of death-associated protein kinase 1 in complex with resveratrol
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / protein kinase / inhibitor / complex / natural compound
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 / 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
Similarity search - Domain/homology
RESVERATROL / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å
AuthorsYokoyama, T. / Suzuki, R. / Mizuguchi, M.
CitationJournal: Iucrj / Year: 2020
Title: Crystal structure of death-associated protein kinase 1 in complex with the dietary compound resveratrol.
Authors: Yokoyama, T. / Suzuki, R. / Mizuguchi, M.
History
DepositionJun 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,1213
Polymers33,7961
Non-polymers3242
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.888, 62.234, 88.248
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 / DAP kinase 1


Mass: 33796.402 Da / Num. of mol.: 1
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-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 35.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.4 M ammonium sulfate, 0.1 M Tris-HCl pH 8.0, 14.4 mg/mL DAPK1, 2 mM resveratrol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.649→41.4 Å / Num. obs: 30997 / % possible obs: 97.3 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 24.1
Reflection shellResolution: 1.649→1.71 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2999 / CC1/2: 0.881 / Rpim(I) all: 0.215 / Rrim(I) all: 0.578

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Processing

Software
NameVersionClassification
PHENIX(1.12-2829_1069: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AUX

5aux


Resolution: 1.649→28.552 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 1549 5 %
Rwork0.1749 --
obs0.1761 30987 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.649→28.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 22 224 2484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062310
X-RAY DIFFRACTIONf_angle_d0.8633122
X-RAY DIFFRACTIONf_dihedral_angle_d19.181871
X-RAY DIFFRACTIONf_chiral_restr0.087344
X-RAY DIFFRACTIONf_plane_restr0.006402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6493-1.70260.26041370.19832605X-RAY DIFFRACTION95
1.7026-1.76340.22081360.19432591X-RAY DIFFRACTION96
1.7634-1.8340.22121380.18162621X-RAY DIFFRACTION97
1.834-1.91740.22461370.17742608X-RAY DIFFRACTION97
1.9174-2.01850.21471390.17142640X-RAY DIFFRACTION97
2.0185-2.14490.18931400.16672656X-RAY DIFFRACTION97
2.1449-2.31050.18241410.16832683X-RAY DIFFRACTION98
2.3105-2.54290.24931410.1822679X-RAY DIFFRACTION98
2.5429-2.91050.21311440.18632723X-RAY DIFFRACTION98
2.9105-3.66570.18641450.17322760X-RAY DIFFRACTION99
3.6657-28.5520.1751510.16812872X-RAY DIFFRACTION98

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