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- PDB-3eh9: Crystal structure of death associated protein kinase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 3eh9
TitleCrystal structure of death associated protein kinase complexed with ADP
ComponentsDeath-associated protein kinase 1DAPK1
KeywordsTRANSFERASE / kinase catalytic domain glycine-rich loop / ANK repeat / Apoptosis / ATP-binding / Calmodulin-binding / Cytoplasm / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
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 / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...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 / calmodulin-dependent protein kinase activity / syntaxin-1 binding / regulation of NMDA receptor activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / negative regulation of translation / postsynaptic density / protein autophosphorylation / 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 / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / 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) ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / 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
ADENOSINE-5'-DIPHOSPHATE / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMcNamara, L.K. / Watterson, D.M. / Brunzelle, J.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structural insight into nucleotide recognition by human death-associated protein kinase.
Authors: McNamara, L.K. / Watterson, D.M. / Brunzelle, J.S.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)34,4144
Polymers33,7941
Non-polymers6193
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.862, 62.675, 88.230
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 / DAPK1 / 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 / Plasmid: pASK-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 1.92 Å3/Da / Density % sol: 35.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: .2 M ammonium iodide 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2008 / Details: Be lenses
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 29383 / Num. obs: 29383 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.08 / Num. unique all: 2895

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1JKS

1jks


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.132 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21706 1489 5.1 %RANDOM
Rwork0.17753 ---
obs0.17955 27835 99.89 %-
all-27835 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.54 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2353 0 46 208 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222456
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9893341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52524.706119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45515444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2031514
X-RAY DIFFRACTIONr_chiral_restr0.1020.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021848
X-RAY DIFFRACTIONr_nbd_refined0.2190.21133
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.225
X-RAY DIFFRACTIONr_mcbond_it0.941.51483
X-RAY DIFFRACTIONr_mcangle_it1.56222372
X-RAY DIFFRACTIONr_scbond_it2.38731077
X-RAY DIFFRACTIONr_scangle_it3.8984.5968
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 115 -
Rwork0.224 2009 -
obs--99.02 %

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