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- PDB-9n2o: Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with... -

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Basic information

Entry
Database: PDB / ID: 9n2o
TitleCrystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-27-040SRM
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / DAPK1 / DAPK1 catalytic subunit / MW01-27-040SRM
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: 1.49 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 MW01-27-040SRM
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,2735
Polymers33,6651
Non-polymers6084
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.850, 62.740, 87.920
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-A1BVL / 5-(pyridin-4-yl)-3-[4-(pyrimidin-2-yl)piperazin-1-yl]pyridazine


Mass: 319.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.92 Å3/Da / Density % sol: 35.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.6M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2022 / Details: Bi-Morph KB Mirrors
RadiationMonochromator: DCM Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.49→29.55 Å / Num. obs: 43096 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Χ2: 0.97 / Net I/σ(I): 13.5 / Num. measured all: 314807
Reflection shellResolution: 1.49→1.53 Å / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.871 / Num. measured all: 22874 / Num. unique obs: 3141 / CC1/2: 0.79 / Rpim(I) all: 0.343 / Rrim(I) all: 0.937 / Χ2: 0.81 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: SIR / Resolution: 1.49→29.55 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 2168 5.04 %Random
Rwork0.1666 ---
obs0.1678 43034 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 39 254 2567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012506
X-RAY DIFFRACTIONf_angle_d1.1623406
X-RAY DIFFRACTIONf_dihedral_angle_d7.202365
X-RAY DIFFRACTIONf_chiral_restr0.099374
X-RAY DIFFRACTIONf_plane_restr0.011446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.32881520.31412652X-RAY DIFFRACTION100
1.52-1.560.251420.25392700X-RAY DIFFRACTION100
1.56-1.610.25031390.21832683X-RAY DIFFRACTION100
1.61-1.650.25181290.2022687X-RAY DIFFRACTION100
1.65-1.710.2311400.18522711X-RAY DIFFRACTION100
1.71-1.770.21991690.18362659X-RAY DIFFRACTION100
1.77-1.840.21431360.18092705X-RAY DIFFRACTION100
1.84-1.920.22211670.1892677X-RAY DIFFRACTION100
1.92-2.020.19261460.16752723X-RAY DIFFRACTION100
2.02-2.150.18131200.16442731X-RAY DIFFRACTION100
2.15-2.310.20251450.16072732X-RAY DIFFRACTION100
2.31-2.550.20731350.16862748X-RAY DIFFRACTION100
2.55-2.920.21561580.16862766X-RAY DIFFRACTION100
2.92-3.670.1691430.15682778X-RAY DIFFRACTION100
3.67-29.550.161470.1512914X-RAY DIFFRACTION100
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)
15.7907-2.68171.9352.1106-2.10512.95660.1138-0.3907-0.21870.28940.1550.32290.1419-0.2812-0.22890.28570.00190.01480.23980.0360.2955-5.7744-3.67226.3388
24.0072-1.62150.67775.219-0.64193.95950.2090.4016-0.2509-0.3312-0.1370.22330.1740.1356-0.0810.2133-0.0035-0.03340.2011-0.00580.2128-7.0976-0.0323-7.4054
34.1773-0.05770.06295.7958-0.11573.71320.0263-0.12-0.4388-0.14280.0807-0.67070.94970.73170.01480.37710.1411-0.01770.3252-0.03780.32359.0624-12.6707-2.8984
42.2842-1.15030.08996.1481-2.11421.82120.1116-0.0211-0.1149-0.1133-0.1438-0.03240.12120.05040.06160.1732-0.01740.00260.1940.01130.14937.08144.8723-1.6555
52.0496-0.31910.43193.3246-0.63582.19210.04690.0696-0.0468-0.0818-0.0273-0.0890.11110.1242-0.06660.1969-0.0206-0.00510.2318-0.00720.2075-1.9974-0.2326-0.4812
62.5229-0.4662-3.49259.32531.54594.92230.07951.145-0.4957-1.6303-0.0745-0.1241-0.0053-0.9572-0.12190.5386-0.0157-0.05820.6458-0.07810.45240.2479.5317-25.6542
77.23021.69312.41277.1667-3.30963.1844-0.22120.09870.4959-0.77260.19390.1977-0.5034-1.11950.04380.36380.04840.04210.35720.06430.31755.408820.8486-24.0449
83.2398-0.4516-0.11042.79090.40673.6621-0.00820.040.04750.0310.0177-0.0228-0.0307-0.0357-0.02740.13830.00280.0160.16160.00680.161111.250613.4134-10.3116
95.5187-1.38761.73094.4004-1.05984.73170.04520.24830.2697-0.2663-0.06250.5138-0.2287-0.46760.03370.17450.00630.00430.22530.01510.20522.237911.6492-13.054
101.76511.13691.83722.4752.20774.10890.3412-0.5472-0.32360.73010.111-0.53290.8243-0.1374-0.36210.33950.0248-0.0810.2730.01740.309820.7273.4844-9.815
111.7419-0.49580.72041.85570.03382.96220.07140.1471-0.12-0.14130.0513-0.01740.09540.1624-0.11540.1471-0.00840.0110.1585-0.00630.175219.22617.5681-24.3827
121.5923-0.33950.10253.21450.02423.77880.02480.03330.1614-0.08690.048-0.0422-0.32010.1343-0.06640.1531-0.04120.02570.1460.01190.189819.965920.6058-20.9033
130.3401-0.8920.24564.49960.8721.3339-0.00630.0051-0.20590.27090.14180.4530.3416-0.3349-0.18170.63140.10590.1770.6984-0.18360.792515.90884.0449-18.3806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 53 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 97 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 110 )
7X-RAY DIFFRACTION7chain 'A' and (resid 111 through 120 )
8X-RAY DIFFRACTION8chain 'A' and (resid 121 through 144 )
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 167 )
10X-RAY DIFFRACTION10chain 'A' and (resid 168 through 184 )
11X-RAY DIFFRACTION11chain 'A' and (resid 185 through 242 )
12X-RAY DIFFRACTION12chain 'A' and (resid 243 through 275 )
13X-RAY DIFFRACTION13chain 'A' and (resid 276 through 294 )

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