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- PDB-9n2m: Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with... -

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Basic information

Entry
Database: PDB / ID: 9n2m
TitleCrystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / DAPK1 / DAPK1 catalytic subunit / MW01-30-047SRM
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
: / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.35 Å
AuthorsBrunzelle, J.S. / Shuvalova, L. / Roy, S.M. / Watterson, D.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM
Authors: Brunzelle, J.S. / Shuvalova, L. / Roy, S.M. / Watterson, D.M.
History
DepositionJan 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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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)34,0803
Polymers33,6651
Non-polymers4142
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.300, 63.080, 88.120
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: 33665.188 Da / Num. of mol.: 1
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)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1BVM / 5-(pyridin-4-yl)-3-[4-(pyridin-4-yl)piperazin-1-yl]pyridazine


Mass: 318.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 37.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M LiSO4, 5% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12705 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 7, 2022 / Details: Bi-morph KB
RadiationMonochromator: DCM Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12705 Å / Relative weight: 1
ReflectionResolution: 1.35→32.24 Å / Num. obs: 57668 / % possible obs: 98.6 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Χ2: 0.96 / Net I/σ(I): 18.7 / Num. measured all: 417722
Reflection shellResolution: 1.35→1.39 Å / % possible obs: 95.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.324 / Num. measured all: 29308 / Num. unique obs: 4079 / CC1/2: 0.96 / Rpim(I) all: 0.127 / Rrim(I) all: 0.349 / Χ2: 0.86 / Net I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimless0.7.8data scaling
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: SIR / Resolution: 1.35→31.54 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1768 2855 4.96 %Random
Rwork0.1444 ---
obs0.1461 57605 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 29 232 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092431
X-RAY DIFFRACTIONf_angle_d1.0883302
X-RAY DIFFRACTIONf_dihedral_angle_d5.685351
X-RAY DIFFRACTIONf_chiral_restr0.094367
X-RAY DIFFRACTIONf_plane_restr0.01442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.20581240.14262630X-RAY DIFFRACTION95
1.37-1.40.18081400.13252626X-RAY DIFFRACTION96
1.4-1.430.20921460.1252659X-RAY DIFFRACTION97
1.43-1.450.16271330.12592685X-RAY DIFFRACTION98
1.45-1.490.16491520.11862687X-RAY DIFFRACTION97
1.49-1.520.17051350.1172723X-RAY DIFFRACTION99
1.52-1.560.18311340.11952731X-RAY DIFFRACTION99
1.56-1.60.18191530.1152705X-RAY DIFFRACTION99
1.6-1.650.16411520.11772707X-RAY DIFFRACTION99
1.65-1.70.15861290.1222735X-RAY DIFFRACTION98
1.7-1.760.16531530.12532745X-RAY DIFFRACTION99
1.76-1.830.17851510.13372757X-RAY DIFFRACTION100
1.83-1.920.15791530.13042754X-RAY DIFFRACTION100
1.92-2.020.16731410.12882764X-RAY DIFFRACTION100
2.02-2.140.14091260.13042815X-RAY DIFFRACTION100
2.14-2.310.17831430.13812782X-RAY DIFFRACTION100
2.31-2.540.1851550.14722810X-RAY DIFFRACTION100
2.54-2.910.19151110.16422781X-RAY DIFFRACTION98
2.91-3.660.181570.15772860X-RAY DIFFRACTION100
3.66-31.540.1821670.15982794X-RAY DIFFRACTION94

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