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- PDB-1yrp: Catalytic domain of human ZIP kinase phosphorylated at Thr265 -

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Basic information

Entry
Database: PDB / ID: 1yrp
TitleCatalytic domain of human ZIP kinase phosphorylated at Thr265
ComponentsDeath-associated protein kinase 3
KeywordsTRANSFERASE / kinase fold / phosphothreonine
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 / small GTPase binding / cellular response to type II interferon / spindle / positive regulation of canonical Wnt signaling pathway / regulation of cell shape / midbody / 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 / regulation of autophagy / negative regulation of translation / intracellular signal transduction / cilium / positive regulation of cell migration / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / apoptotic process / centrosome / regulation of DNA-templated transcription / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Death-associated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKursula, P. / Vahokoski, J. / Wilmanns, M.
CitationJournal: Structure / Year: 2016
Title: Death-Associated Protein Kinase Activity Is Regulated by Coupled Calcium/Calmodulin Binding to Two Distinct Sites
Authors: Simon, B. / Huart, A.S. / Temmerman, K. / Vahokoski, J. / Mertens, H.D. / Komadina, D. / Hoffmann, J.E. / Yumerefendi, H. / Svergun, D.I. / Kursula, P. / Schultz, C. / McCarthy, A.A. / Hart, D.J. / Wilmanns, M.
History
DepositionFeb 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 18, 2016Group: Database references
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,2733
Polymers64,1192
Non-polymers1541
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-10 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.560, 60.930, 87.950
Angle α, β, γ (deg.)90.00, 92.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 2 - 277 / Label seq-ID: 3 - 278

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 32059.402 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDEST-15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: O43293, EC: 2.7.1.37
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: PEG, MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 10171 / Num. obs: 10171 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.098 / Net I/σ(I): 11.3
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 900 / Rsym value: 0.336 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.849 / SU B: 62.478 / SU ML: 0.503 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS REFINEMENT / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R Free: 0.582 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26842 509 5 %RANDOM
Rwork0.24383 ---
all0.24508 10171 --
obs0.24508 10171 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.425 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-2.3 Å2
2--4.69 Å20 Å2
3----4.03 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 8 0 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224583
X-RAY DIFFRACTIONr_bond_other_d0.0020.024201
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9716176
X-RAY DIFFRACTIONr_angle_other_deg1.25939791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18224.174230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40815854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7941534
X-RAY DIFFRACTIONr_chiral_restr0.0590.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025038
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02936
X-RAY DIFFRACTIONr_nbd_refined0.2010.2900
X-RAY DIFFRACTIONr_nbd_other0.1690.24220
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22134
X-RAY DIFFRACTIONr_nbtor_other0.0830.22674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.28
X-RAY DIFFRACTIONr_mcbond_it0.10123589
X-RAY DIFFRACTIONr_mcbond_other0.04121122
X-RAY DIFFRACTIONr_mcangle_it0.14834446
X-RAY DIFFRACTIONr_scbond_it0.2142106
X-RAY DIFFRACTIONr_scangle_it0.31651730
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4342 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.010.5
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 35 -
Rwork0.325 673 -
obs--95.29 %
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)
14.33371.220.96261.4481-0.28321.00840.0911-0.2185-0.01580.0757-0.09160.16650.0762-0.1130.0006-0.14650.03750.0393-0.1889-0.0046-0.20220.55920.082228.6464
21.2955-0.7735-0.4051.65191.24793.9118-0.0252-0.16570.06930.058-0.09970.1506-0.0952-0.4070.1249-0.1581-0.0178-0.0044-0.15550.0649-0.104610.324824.488612.1161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2773 - 278
2X-RAY DIFFRACTION2BB2 - 2773 - 278

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