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- PDB-6ft9: Crystal structure of CLK1 in complex with inhibitor 16 -

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Basic information

Entry
Database: PDB / ID: 6ft9
TitleCrystal structure of CLK1 in complex with inhibitor 16
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / kinase / inhibitor / splicing kinase / CLK / Structural Genomics / Structural Genomics Consortium / SGC
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 / 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
BROMIDE ION / Chem-E6W / PHOSPHATE ION / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 CLK1
B: Dual specificity protein kinase CLK1
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,77420
Polymers118,7453
Non-polymers2,03017
Water9,980554
1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3818
Polymers39,5821
Non-polymers7997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1976
Polymers39,5821
Non-polymers6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1976
Polymers39,5821
Non-polymers6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.400, 116.301, 91.330
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA0 - 4812 - 336
21METMETBB0 - 4812 - 336
12METMETAA0 - 4812 - 336
22METMETCC0 - 4812 - 336
13SERSERBB-1 - 4821 - 337
23SERSERCC-1 - 4821 - 337

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39581.512 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 / References: UniProt: P49759, dual-specificity kinase

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Non-polymers , 6 types, 571 molecules

#2: Chemical ChemComp-E6W / 2-bromanyl-3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one


Mass: 325.159 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H9BrN2O
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% 1,2-propanediol, 10% glycerol, 0.1 M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.87→29.11 Å / Num. obs: 95883 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.9
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2 / Num. unique obs: 13962 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J1W

5j1w


Resolution: 1.87→29.11 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.213 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20167 4748 5 %RANDOM
Rwork0.16635 ---
obs0.1681 91087 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.145 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-0 Å2-0.57 Å2
2--1.49 Å20 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.87→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8264 0 111 554 8929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198688
X-RAY DIFFRACTIONr_bond_other_d0.0080.028150
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.94311764
X-RAY DIFFRACTIONr_angle_other_deg1.204318760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76551019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60823.325424
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55151510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8981559
X-RAY DIFFRACTIONr_chiral_restr0.0990.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210250
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022107
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_it2.0662.3054049
X-RAY DIFFRACTIONr_mcbond_other2.0662.3054050
X-RAY DIFFRACTIONr_mcangle_it2.9283.4445059
X-RAY DIFFRACTIONr_mcangle_other2.9293.4445060
X-RAY DIFFRACTIONr_scbond_it3.1192.7534639
X-RAY DIFFRACTIONr_scbond_other3.1172.7534639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7783.9796700
X-RAY DIFFRACTIONr_long_range_B_refined7.53320.0110293
X-RAY DIFFRACTIONr_long_range_B_other7.53320.01310294
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)
11A215250.07
12B215250.07
21A208590.09
22C208590.09
31B208310.1
32C208310.1
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 359 -
Rwork0.279 6689 -
obs--99.94 %
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)
12.51380.1284-1.14071.26730.07842.02270.02570.0794-0.1362-0.1679-0.04380.00820.1045-0.14380.01810.03930.0065-0.01050.06080.00810.019246.365827.802572.3154
22.73880.6203-0.10861.3467-0.26321.49990.0634-0.1730.02850.045-0.0015-0.09360.07810.0463-0.06190.02760.03920.01580.09270.03570.038357.603-17.574969.4076
33.2919-1.4417-0.64791.85020.44921.4221-0.0729-0.01940.086-0.01540.06180.0427-0.08080.10360.01110.0166-0.01460.00230.0152-0.00350.018139.5967-0.616436.6787
42.4613-0.57240.23614.80570.52573.5248-0.1363-0.10130.39790.18930.13520.062-0.6774-0.11050.00110.15090.0350.00840.0986-0.00640.192522.450515.549641.4111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 482
2X-RAY DIFFRACTION2B-1 - 482
3X-RAY DIFFRACTION3C-1 - 372
4X-RAY DIFFRACTION4C373 - 482

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