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- PDB-2j90: Crystal structure of human ZIP kinase in complex with a tetracycl... -

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Basic information

Entry
Database: PDB / ID: 2j90
TitleCrystal structure of human ZIP kinase in complex with a tetracyclic pyridone inhibitor (Pyridone 6)
ComponentsDEATH-ASSOCIATED PROTEIN KINASE 3
KeywordsTRANSFERASE / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / SERINE/THREONINE- PROTEIN KINASE / CHROMATIN REGULATOR / MYOSIN PHOSPHORYLATION / KINASE / MUSCLE / APOPTOSIS / ATP-BINDING
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 / 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 / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / intracellular signal transduction / regulation of autophagy / cilium / positive regulation of cell migration / positive regulation of apoptotic process / protein serine kinase activity / intracellular membrane-bounded organelle / 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-IZA / PHOSPHATE ION / Death-associated protein kinase 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTurnbull, A.P. / Berridge, G. / Fedorov, O. / Pike, A.C.W. / Savitsky, P. / Eswaran, J. / Papagrigoriou, E. / Ugochukwa, E. / von Delft, F. / Gileadi, O. ...Turnbull, A.P. / Berridge, G. / Fedorov, O. / Pike, A.C.W. / Savitsky, P. / Eswaran, J. / Papagrigoriou, E. / Ugochukwa, E. / von Delft, F. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Knapp, S.
CitationJournal: Embo J. / Year: 2008
Title: Activation Segment Dimerization: A Mechanism for Kinase Autophosphorylation of Non-Consensus Sites.
Authors: Pike, A.C.W. / Rellos, P. / Niesen, F.H. / Turnbull, A. / Oliver, A.W. / Parker, S.A. / Turk, B.E. / Pearl, L.H. / Knapp, S.
History
DepositionOct 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)71,32410
Polymers70,3532
Non-polymers9718
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.765, 95.765, 150.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92836, -0.31836, -0.19183), (-0.35011, 0.57573, 0.73889), (-0.12479, 0.75312, -0.64594)
Vector: 76.86736, 18.85642, -7.42233)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DEATH-ASSOCIATED PROTEIN KINASE 3 / DAP KINASE 3 / DAP-LIKE KINASE / DLK / ZIP KINASE


Mass: 35176.742 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 9-289
Source method: isolated from a genetically manipulated source
Details: DIPHOSPHORYLATED FORM (SER50 AND THR265) / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: O43293, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 335 molecules

#2: Chemical ChemComp-IZA / 2-TERT-BUTYL-9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLINE-7-ONE / 2-(1,1-DIMETHYLETHYL)9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLIN-7-ONE


Mass: 309.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16FN3O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growpH: 8 / Details: 30% PEG 1000 0.1M SPG BUFFER PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 48089 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1YRP, 1JKT, 1JKS, 1WVX

1yrp

1jkt

1jks

1wvx


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.201 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2433 5.1 %RANDOM
Rwork0.185 ---
obs0.187 45599 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 65 327 4581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224388
X-RAY DIFFRACTIONr_bond_other_d0.0010.022965
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9875937
X-RAY DIFFRACTIONr_angle_other_deg1.2393.0017224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1695530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91224.307202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70515.039771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2021526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02876
X-RAY DIFFRACTIONr_nbd_refined0.1970.2801
X-RAY DIFFRACTIONr_nbd_other0.180.22945
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22111
X-RAY DIFFRACTIONr_nbtor_other0.0820.22229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.74232779
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55654281
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.99872028
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.859111656
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 171
Rwork0.226 3308
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)
13.84440.2630.54482.67510.16973.8177-0.0549-0.3050.26430.1314-0.01320.0784-0.1250.16840.0681-0.06650.0195-0.0268-0.1668-0.0342-0.128230.586815.703618.499
21.39750.10630.68532.071.03761.8439-0.0128-0.2332-0.06840.2571-0.16230.35460.1935-0.35990.1751-0.1133-0.01110.0414-0.0992-0.0144-0.098618.52363.07311.0635
35.4382-0.4945-5.36120.46750.5646.57070.08520.54270.1128-0.02290.0230.0538-0.2829-0.3901-0.1082-0.1389-0.0291-0.0313-0.1433-0.0028-0.149233.63336.1817-4.6112
42.50730.8153-0.63612.8512-0.48422.09010.0004-0.0012-0.2544-0.06260.01340.13780.1535-0.0453-0.0137-0.1069-0.03820.007-0.1863-0.0403-0.131723.8525-11.6728-0.9821
56.7564-0.91290.77280.88710.51552.6472-0.10690.27790.6155-0.18880.11860.3499-0.5007-0.566-0.01170.15790.1665-0.00030.1520.0330.165638.86728.0862-13.2191
63.72-0.54210.1132.94340.0532.73160.04830.2020.7105-0.12210.023-0.2203-0.5559-0.0323-0.0713-0.0524-0.0249-0.01-0.07180.02940.014955.423221.9714-12.9204
73.0824-0.8751.61952.35982.66695.4807-0.0759-0.03540.3366-0.1187-0.0886-0.5283-0.41560.30140.1645-0.0470.00250.0113-0.02250.0017-0.050536.4176-2.41624.5751
83.35540.63640.58682.42420.40761.2661-0.02270.4643-0.1838-0.19830.0579-0.36910.02830.2986-0.0352-0.1547-0.03040.027-0.0153-0.0387-0.076358.86883.7799-18.954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 71
2X-RAY DIFFRACTION2A72 - 155
3X-RAY DIFFRACTION3A156 - 190
4X-RAY DIFFRACTION4A191 - 278
5X-RAY DIFFRACTION5B12 - 66
6X-RAY DIFFRACTION6B67 - 168
7X-RAY DIFFRACTION7B169 - 190
8X-RAY DIFFRACTION8B191 - 280

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