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- PDB-5vja: Crystal Structure of human zipper-interacting protein kinase (ZIP... -

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Basic information

Entry
Database: PDB / ID: 5vja
TitleCrystal Structure of human zipper-interacting protein kinase (ZIPK, alias DAPK3) in complex with a pyrazolo[3,4-d]pyrimidinone ligand (HS38)
ComponentsDeath-associated protein kinase 3
Keywordstransferase/transferase inhibitor / death-associated protein kinase 3 / transferase / inhibitor / smooth muscle contraction / transferase-transferase inhibitor complex
Function / homology
Function and homology information


regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / regulation of cell motility / Caspase activation via Dependence Receptors in the absence of ligand / regulation of focal adhesion assembly / regulation of mitotic nuclear division / chromosome, centromeric region / regulation of mitotic cell cycle ...regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / regulation of cell motility / Caspase activation via Dependence Receptors in the absence of ligand / regulation of focal adhesion assembly / regulation of mitotic nuclear division / chromosome, centromeric region / regulation of mitotic cell cycle / regulation of actin cytoskeleton organization / apoptotic signaling pathway / PML body / regulation of autophagy / cellular response to type II interferon / small GTPase binding / spindle / positive regulation of canonical Wnt signaling pathway / regulation of cell shape / protein autophosphorylation / chromatin organization / midbody / regulation of apoptotic process / protein phosphorylation / protein kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / negative regulation of translation / cilium / positive regulation of cell migration / positive regulation of apoptotic process / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / regulation of DNA-templated transcription / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DAPK3, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...DAPK3, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DUK / ISOLEUCINE / Death-associated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsCarlson, D.A. / Singer, M.R. / Sutherland, C. / Redondo, C. / Alexander, L. / Hughes, P.F. / Knapp, S. / MacDonald, J.A. / Haystead, T.A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Mandel Foundation United States
CitationJournal: Cell Chem Biol / Year: 2018
Title: Targeting Pim Kinases and DAPK3 to Control Hypertension.
Authors: Carlson, D.A. / Singer, M.R. / Sutherland, C. / Redondo, C. / Alexander, L.T. / Hughes, P.F. / Knapp, S. / Gurley, S.B. / Sparks, M.A. / MacDonald, J.A. / Haystead, T.A.J.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Death-associated protein kinase 3
B: Death-associated protein kinase 3
C: Death-associated protein kinase 3
D: Death-associated protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,02313
Polymers130,1804
Non-polymers1,8439
Water8,575476
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint5 kcal/mol
Surface area51240 Å2
Unit cell
Length a, b, c (Å)53.492, 98.491, 115.022
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA7 - 2771 - 271
21ALAALABB7 - 2771 - 271
12ALAALAAA7 - 2771 - 271
22ALAALACC7 - 2771 - 271
13ALAALAAA7 - 2771 - 271
23ALAALADD7 - 2771 - 271
14ILEILEBB7 - 2781 - 272
24ILEILECC7 - 2781 - 272
15ALAALABB7 - 2771 - 271
25ALAALADD7 - 2771 - 271
16ALAALACC7 - 2771 - 271
26ALAALADD7 - 2771 - 271

NCS ensembles :
ID
2
1
3
4
5
6

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Components

#1: Protein
Death-associated protein kinase 3 / DAP kinase 3 / DAP-like kinase / Dlk / MYPT1 kinase / Zipper-interacting protein kinase / ZIP-kinase


Mass: 32545.123 Da / Num. of mol.: 4 / Fragment: UNP residues 9-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK3, ZIPK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O43293, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-DUK / (2R)-2-{[1-(3-chlorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}propanamide


Mass: 349.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12ClN5O2S
#4: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.9 M Na2-Malonate, pH 6.8 / PH range: 6.8 - 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2014
RadiationMonochromator: Si [111] CCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.46→115.02 Å / Num. obs: 42067 / % possible obs: 97 % / Redundancy: 3.2 % / Net I/σ(I): 6.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLM7.1.1data reduction
SCALA3.3.22data scaling
AMoRE6.5.001phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P4F

1p4f


Resolution: 2.46→115.02 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 18.85 / SU ML: 0.222 / Cross valid method: FREE R-VALUE / ESU R: 0.789 / ESU R Free: 0.287 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2092 5 %RANDOM
Rwork0.18764 ---
obs0.19001 39975 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å21.81 Å2
2---0.42 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.46→115.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8566 0 116 476 9158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198850
X-RAY DIFFRACTIONr_bond_other_d0.0030.028371
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9811919
X-RAY DIFFRACTIONr_angle_other_deg1.018319411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91451048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99124.408431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.311151642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.421557
X-RAY DIFFRACTIONr_chiral_restr0.1020.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029651
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021798
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7981.714225
X-RAY DIFFRACTIONr_mcbond_other1.7981.7114226
X-RAY DIFFRACTIONr_mcangle_it2.9312.5515263
X-RAY DIFFRACTIONr_mcangle_other2.9292.5535263
X-RAY DIFFRACTIONr_scbond_it2.3742.0154625
X-RAY DIFFRACTIONr_scbond_other2.3612.0144624
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5232.9156656
X-RAY DIFFRACTIONr_long_range_B_refined6.18620.5449777
X-RAY DIFFRACTIONr_long_range_B_other6.15720.3329693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A168040.07
12B168040.07
21A157400.11
22C157400.11
31A157000.11
32D157000.11
41B158700.11
42C158700.11
51B156460.11
52D156460.11
61C165020.07
62D165020.07
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 161 -
Rwork0.262 2919 -
obs--96.37 %
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)
11.8834-1.0894-0.89932.7651.70981.87710.01940.0983-0.0181-0.0604-0.0555-0.04320.03610.05720.03610.1328-0.02-0.12710.02630.03930.1485-29.1838-0.338255.0273
21.7160.97520.68452.95361.29371.9940.055-0.10470.00460.0255-0.0366-0.0551-0.08340.0733-0.01840.0681-0.0302-0.08240.02090.02590.1177-29.032610.84232.4281
33.1554-1.1966-2.5760.85220.98373.87690.2209-0.02770.28380.02180.01570.0462-0.6248-0.0631-0.23670.2737-0.0136-0.05620.0730.01980.2083-3.8609-19.416418.0293
42.36060.63011.66821.04720.86033.31220.1505-0.0316-0.2178-0.0271-0.01520.06390.5307-0.1151-0.13530.17620.008-0.08990.09380.01850.1301-3.793330.087439.4492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 277
2X-RAY DIFFRACTION2B7 - 277
3X-RAY DIFFRACTION3C7 - 277
4X-RAY DIFFRACTION4D7 - 277

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