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- PDB-5av3: Crystal structure of DAPK1-kaempferol complex in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 5av3
TitleCrystal structure of DAPK1-kaempferol complex in the presence of iodide ions.
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / death-associated protein kinase 1 / serine/threonine protein kinase / natural flavonoid
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 / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : ...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 / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / postsynaptic density / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / apoptotic process / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Chem-KMP / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsYokoyama, T. / Mizuguchi, M.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structural Insight into the Interactions between Death-Associated Protein Kinase 1 and Natural Flavonoids.
Authors: Yokoyama, T. / Kosaka, Y. / Mizuguchi, M.
History
DepositionJun 10, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)35,22511
Polymers33,7961
Non-polymers1,42810
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.884, 62.357, 88.329
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 / Fragment: UNP RESIDUES 1-285
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-KMP / 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE / KAEMPHEROL


Mass: 286.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O6
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M ammonium sulfate, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 1.9→44.2 Å / Num. obs: 20853 / % possible obs: 98.9 % / Redundancy: 10 % / Net I/σ(I): 76.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
RefinementResolution: 1.9→44.164 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1064 5.13 %
Rwork0.1825 --
obs0.1851 20727 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 30 209 2468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042297
X-RAY DIFFRACTIONf_angle_d0.9513104
X-RAY DIFFRACTIONf_dihedral_angle_d14.887878
X-RAY DIFFRACTIONf_chiral_restr0.064342
X-RAY DIFFRACTIONf_plane_restr0.004398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.98690.28291230.18752333X-RAY DIFFRACTION96
1.9869-2.09170.21191290.17382393X-RAY DIFFRACTION98
2.0917-2.22270.22071300.17142444X-RAY DIFFRACTION98
2.2227-2.39440.23291380.18532411X-RAY DIFFRACTION99
2.3944-2.63530.25181410.18752460X-RAY DIFFRACTION99
2.6353-3.01650.26331200.19442499X-RAY DIFFRACTION100
3.0165-3.80020.22981340.18312513X-RAY DIFFRACTION100
3.8002-44.17640.2141490.17752610X-RAY DIFFRACTION99

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