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- PDB-2vag: Crystal structure of di-phosphorylated human CLK1 in complex with... -

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Basic information

Entry
Database: PDB / ID: 2vag
TitleCrystal structure of di-phosphorylated human CLK1 in complex with a novel substituted indole inhibitor
ComponentsDUAL SPECIFICITY PROTEIN KINASE CLK1
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE / NUCLEUS
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
: / 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 ...: / 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-V25 / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPike, A.C.W. / Bullock, A.N. / Fedorov, O. / Pilka, E.S. / Ugochukwu, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. ...Pike, A.C.W. / Bullock, A.N. / Fedorov, O. / Pilka, E.S. / Ugochukwu, E. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Huber, K. / Bracher, F. / Knapp, S.
CitationJournal: Chem.Biol / Year: 2011
Title: Specific Clk Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing.
Authors: Fedorov, O. / Huber, K. / Eisenreich, A. / Filippakopoulos, P. / King, O. / Bullock, A.N. / Szklarczyk, D. / Jensen, L.J. / Fabbro, D. / Trappe, J. / Rauch, U. / Bracher, F. / Knapp, S.
History
DepositionAug 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references / Structure summary
Revision 1.3Dec 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUAL SPECIFICITY PROTEIN KINASE CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0802
Polymers39,7411
Non-polymers3381
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.950, 64.108, 78.894
Angle α, β, γ (deg.)90.00, 118.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DUAL SPECIFICITY PROTEIN KINASE CLK1 / CDC-LIKE KINASE 1


Mass: 39741.469 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 148-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-V25 / ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate


Mass: 338.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13Cl2N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.9 % / Description: NONE
Crystal growpH: 7 / Details: 2.1M SODIUM MALATE PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.006029
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006029 Å / Relative weight: 1
ReflectionResolution: 1.8→33.58 Å / Num. obs: 36979 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 25.45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z57

1z57


Resolution: 1.8→32 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.058 / SU ML: 0.096 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1887 5.1 %RANDOM
Rwork0.18 ---
obs0.182 35072 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-1.05 Å2
2---0.32 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 22 230 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212735
X-RAY DIFFRACTIONr_bond_other_d0.0010.021803
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9553717
X-RAY DIFFRACTIONr_angle_other_deg1.0043.0014365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46623.359128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71815.034441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8861516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02577
X-RAY DIFFRACTIONr_nbd_refined0.2030.2593
X-RAY DIFFRACTIONr_nbd_other0.1870.21913
X-RAY DIFFRACTIONr_nbtor_refined0.180.21352
X-RAY DIFFRACTIONr_nbtor_other0.0960.21312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.48531700
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.65152673
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.59781197
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.659111044
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 150
Rwork0.265 2572
Refinement TLS params.Method: refined / Origin x: 14.527 Å / Origin y: 6.827 Å / Origin z: 14.938 Å
111213212223313233
T-0.0179 Å20.0663 Å2-0.0426 Å2--0.0879 Å2-0.0067 Å2---0.1231 Å2
L0.7934 °20.2247 °2-0.2626 °2-1.5628 °20.3152 °2--1.291 °2
S-0.1673 Å °-0.0795 Å °-0.0351 Å °-0.2754 Å °0.0597 Å °0.0512 Å °-0.2866 Å °-0.0779 Å °0.1076 Å °

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