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- PDB-6ft7: Crystal structure of CLK3 in complex with compound 8a -

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Basic information

Entry
Database: PDB / ID: 6ft7
TitleCrystal structure of CLK3 in complex with compound 8a
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / kinase / inhibitor / splicing kinase / CLK / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / Alpha Beta
Similarity search - Domain/homology
3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one / IODIDE ION / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsChaikuad, A. / Walter, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kunick, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: PLoS ONE / Year: 2018
Title: Molecular structures of cdc2-like kinases in complex with a new inhibitor chemotype.
Authors: Walter, A. / Chaikuad, A. / Helmer, R. / Loaec, N. / Preu, L. / Ott, I. / Knapp, S. / Meijer, L. / Kunick, C.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Dual specificity protein kinase CLK3
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,65130
Polymers84,6372
Non-polymers3,01428
Water8,737485
1
A: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,63912
Polymers42,3181
Non-polymers1,32111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,01218
Polymers42,3181
Non-polymers1,69317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.760, 116.830, 69.910
Angle α, β, γ (deg.)90.00, 92.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA129 - 2375 - 113
21SERSERGLUGLUBB129 - 2375 - 113
12LEULEUARGARGAA238 - 480114 - 356
22LEULEUARGARGBB238 - 480114 - 356

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999991, 0.003927, 0.001666), (-0.003969, -0.999653, -0.026031), (0.001563, -0.026037, 0.99966)88.80568, 148.12427, 1.89425
3given(1), (1), (1)
4given(-0.999918, 0.008771, 0.00928), (-0.008914, -0.999839, -0.015566), (0.009142, -0.015647, 0.999836)87.96809, 147.70662, 0.53903

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Components

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 42318.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 / References: UniProt: P49761, dual-specificity kinase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-E6Q / 3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one


Mass: 246.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% PEG3350, 0.2 M sodium iodide, 0.1 M bis-tris-propane pH 7.0, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→59.95 Å / Num. obs: 62659 / % possible obs: 96.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8
Reflection shellResolution: 2.02→2.13 Å / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9103 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EU9

2eu9


Resolution: 2.02→58.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.305 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23523 3185 5.1 %RANDOM
Rwork0.1917 ---
obs0.19395 59444 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.86 Å20 Å2-0.21 Å2
2--1.57 Å20 Å2
3---1.27 Å2
Refinement stepCycle: 1 / Resolution: 2.02→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 100 485 6385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196144
X-RAY DIFFRACTIONr_bond_other_d0.0010.024272
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.948301
X-RAY DIFFRACTIONr_angle_other_deg0.96310335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65523.491318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.748151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391544
X-RAY DIFFRACTIONr_chiral_restr0.0980.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021349
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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_free47.09257
X-RAY DIFFRACTIONr_sphericity_bonded83.63957
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1441medium positional0.330.5
22B3387medium positional0.280.5
11A1441medium thermal2.142
22B3387medium thermal2.432
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 206 -
Rwork0.303 4311 -
obs--95.5 %
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)
12.34090.28490.5591.6057-0.58381.0072-0.14890.24860.43280.22590.0087-0.1737-0.02680.03710.14020.08430.0086-0.05870.10.04290.293158.35574.181555.9968
21.1253-0.1998-0.29190.45840.35930.444-0.03250.2265-0.17190.1418-0.07110.00430.0299-0.08030.10350.1143-0.012-0.00310.1716-0.02170.129457.682147.348848.8938
39.6622-11.143111.292324.79944.956840.4378-0.9498-1.87661.15660.91010.269-1.3358-0.4365-3.99710.68080.7371-0.60950.41251.4658-0.45450.617257.068144.162170.7614
41.5852-1.1184-2.8672.17791.49655.4149-0.36910.4596-0.34160.4102-0.22860.58320.6164-0.94390.59770.1305-0.17110.14090.3684-0.26970.756825.014162.73749.807
51.4559-0.1111-0.37920.7575-0.26310.3119-0.03550.1447-0.16860.0933-0.0680.0509-0.027-0.05340.10350.088-0.0031-0.00780.1696-0.01840.136831.040887.54355.4815
61.639-0.48620.8880.217-0.37541.7112-0.01790.30840.45510.0764-0.0884-0.0728-0.07220.0450.10630.1034-0.02360.00740.14450.11120.241832.7425107.675444.9064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A129 - 215
2X-RAY DIFFRACTION2A216 - 472
3X-RAY DIFFRACTION3A473 - 484
4X-RAY DIFFRACTION4B129 - 147
5X-RAY DIFFRACTION5B148 - 368
6X-RAY DIFFRACTION6B369 - 484

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