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- PDB-7opg: Crystal structure of CLK1 in complex with compound 2 (CC513) -

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Basic information

Entry
Database: PDB / ID: 7opg
TitleCrystal structure of CLK1 in complex with compound 2 (CC513)
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / kinase inhibitor / CLK1 / splicing kinase / 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 / histone H2AXY142 kinase activity / histone H3Y41 kinase activity / protein tyrosine kinase activity / protein serine/threonine kinase activity / protein serine kinase activity / ATP binding / nucleus
Similarity search - Function
: / 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
Similarity search - Domain/homology
Chem-06N / PHOSPHATE ION / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsChaikuad, A. / Routier, S. / Bonnet, P. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of CLK1 in complex with compound 2 (CC513)
Authors: Chaikuad, A. / Routier, S. / Bonnet, P. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMay 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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)120,91719
Polymers118,7453
Non-polymers2,17216
Water11,151619
1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2246
Polymers39,5821
Non-polymers6435
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)40,5588
Polymers39,5821
Non-polymers9767
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)40,1355
Polymers39,5821
Non-polymers5534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.390, 116.930, 91.800
Angle α, β, γ (deg.)90.000, 99.040, 90.000
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: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-1 - 4811 - 336
21BB-1 - 4811 - 336
12AA-1 - 4821 - 337
22CC-1 - 4821 - 337
13BB-1 - 4811 - 336
23CC-1 - 4811 - 336

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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: P49759, dual-specificity kinase

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Non-polymers , 5 types, 635 molecules

#2: Chemical ChemComp-06N / 4-[2-(propylamino)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]phenol


Mass: 274.341 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H14N4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 25% 1,2-propanediol, 10% glycerol, 0.1M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.93→31.01 Å / Num. obs: 88084 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.051 / Rrim(I) all: 0.125 / Net I/av σ(I): 8.2 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.93-2.035.70.7072.1128400.6920.3210.7780.70799.9
2.03-2.165.50.4891.5121320.2250.540.489100
2.16-2.315.60.4321.4113850.1970.4760.43299.9
2.31-2.495.70.2732.7106470.1230.30.27399.9
2.49-2.735.60.1953.797790.0890.2150.195100
2.73-3.055.70.1395.188460.0630.1530.13999.9
3.05-3.525.70.097.378790.0410.0990.0999.9
3.52-4.325.70.068966090.0310.0750.068100
4.32-6.15.60.069.951350.0270.0660.0699.9
6.1-29.5545.50.05410.128320.0240.0590.05498.9

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z57

1z57


Resolution: 1.93→31.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.734 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1512 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 4356 5 %RANDOM
Rwork0.1748 ---
obs0.1764 83367 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.85 Å2 / Biso mean: 41.413 Å2 / Biso min: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å2-0.72 Å2
2--1.52 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.93→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8280 0 142 619 9041
Biso mean--46.74 43.84 -
Num. residues----1012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198691
X-RAY DIFFRACTIONr_bond_other_d0.0070.028198
X-RAY DIFFRACTIONr_angle_refined_deg1.571.95111749
X-RAY DIFFRACTIONr_angle_other_deg1.159318886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72851027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11723.333426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.414151517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9591559
X-RAY DIFFRACTIONr_chiral_restr0.0950.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029902
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022089
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A211710.08
12B211710.08
21A214410.08
22C214410.08
31B210320.09
32C210320.09
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 323 -
Rwork0.287 6168 -
all-6491 -
obs--99.97 %
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)
13.13940.0794-1.23210.8259-0.14552.21540.0889-0.0506-0.16190.0454-0.1032-0.10390.14690.16150.01430.07170.0045-0.03510.15180.00130.030850.5811.98458.858
21.7508-0.44720.36293.642-0.59353.8011-0.0098-0.2433-0.16790.6665-0.0190.25970.1018-0.18270.02880.1501-0.07580.04730.24520.00910.08932.5430.81173.899
33.5564-1.4044-0.33342.1430.40291.6649-0.04570.0949-0.0085-0.08580.02740.0925-0.04970.12750.01830.0148-0.0241-0.00890.05280.01110.006534.0829.5680.432
42.6715-1.28340.60393.67330.2484.5161-0.2403-0.17260.47350.15210.13280.0489-0.6818-0.02810.10760.1190.0288-0.01810.13630.00030.186117.15146.27887.564
54.90150.33290.93752.43710.77183.18170.01830.02790.172-0.0109-0.0132-0.2069-0.00840.3168-0.00510.053200.05160.17750.05180.087967.07424.277111.192
62.25950.1567-0.45242.25870.01183.04260.0674-0.2471-0.04090.13130.07550.00010.2969-0.1404-0.14290.0450.0028-0.00950.20510.06270.022943.81110.673116.555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 388
2X-RAY DIFFRACTION2A389 - 482
3X-RAY DIFFRACTION3B-1 - 336
4X-RAY DIFFRACTION4B337 - 483
5X-RAY DIFFRACTION5C-1 - 245
6X-RAY DIFFRACTION6C246 - 482

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