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- PDB-6z52: Crystal structure of CLK3 in complex with macrocycle ODS2003136 -

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Basic information

Entry
Database: PDB / ID: 6z52
TitleCrystal structure of CLK3 in complex with macrocycle ODS2003136
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / kinase / kinase inhibitor / clk3 / macrocycle / nanocyclic / 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 / protein phosphorylation / nuclear speck / 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 / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane
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
IODIDE ION / Chem-Q8T / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsChaikuad, A. / Benderitter, P. / Hoflack, J. / Denis, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of CLK3 in complex with macrocycle ODS2003136
Authors: Chaikuad, A. / Benderitter, P. / Hoflack, J. / Denis, A. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionMay 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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)88,13332
Polymers84,6372
Non-polymers3,49630
Water10,359575
1
A: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,06716
Polymers42,3181
Non-polymers1,74815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,06716
Polymers42,3181
Non-polymers1,74815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.168, 116.909, 71.161
Angle α, β, γ (deg.)90.000, 93.150, 90.000
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(-0.999999, 7.7E-5, -0.001312), (-8.8E-5, -0.999963, 0.008598), (-0.001311, 0.008598, 0.999962)27.24032, 20.76902, -0.10469
3given(1), (1), (1)
4given(-0.999994, -0.003274, 0.001185), (0.003281, -0.999975, 0.006332), (0.001164, 0.006336, 0.999979)27.303341, 20.725559, -0.04421

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Components

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Protein , 1 types, 2 molecules AB

#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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 / References: UniProt: P49761, dual-specificity kinase

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Non-polymers , 5 types, 605 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-Q8T / 11,15-dimethyl-6-(4-methylpiperazin-1-yl)-8-oxa-2,11,15,19,21,23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one


Mass: 478.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H34N8O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20.0% PEG 3350, 0.20M NaI, 0.1M bis-tris propane pH 7.5, 10.0% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.12→19.87 Å / Num. obs: 55923 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.093 / Rrim(I) all: 0.175 / Net I/av σ(I): 4.4 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.12-2.233.60.653282910.4040.770.65398.8
2.23-2.373.50.4491.778660.280.5310.44998.8
2.37-2.533.40.3442.173270.2180.4090.34498.9
2.53-2.743.10.248366190.1660.2990.24895.7
2.74-33.50.1893.963100.1180.2240.18998.7
3-3.353.50.1295.656750.0810.1530.12998
3.35-3.873.40.0976.849000.0610.1150.09795.9
3.87-4.743.20.0787.741070.0510.0940.07894.9
4.74-6.73.30.0757.931150.0480.090.07593.2
6.7-19.6553.70.0717.817130.0420.0830.07191

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2eu9

2eu9


Resolution: 2.12→19.58 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.587 / SU ML: 0.131 / SU R Cruickshank DPI: 0.1942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 2839 5.1 %RANDOM
Rwork0.1779 ---
obs0.1806 53056 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.79 Å2 / Biso mean: 22.885 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å2-0.02 Å2
2--0.35 Å20 Å2
3---0.97 Å2
Refinement stepCycle: final / Resolution: 2.12→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5836 0 130 575 6541
Biso mean--29.07 34.16 -
Num. residues----708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196201
X-RAY DIFFRACTIONr_bond_other_d0.0010.024368
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9458367
X-RAY DIFFRACTIONr_angle_other_deg0.932310565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39223.458321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.628151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5791547
X-RAY DIFFRACTIONr_chiral_restr0.0980.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021349
X-RAY DIFFRACTIONr_sphericity_free22.88159
X-RAY DIFFRACTIONr_sphericity_bonded22.963511
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11511MEDIUM POSITIONAL0.220.5
11511MEDIUM THERMAL1.792
23495MEDIUM POSITIONAL0.210.5
23495MEDIUM THERMAL2.572
LS refinement shellResolution: 2.12→2.174 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 213 -
Rwork0.277 3858 -
all-4071 -
obs--98.48 %
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)
10.50870.299-0.01170.41340.19160.3574-0.0566-0.06330.0648-0.1353-0.01320.0502-0.0324-0.01640.06980.0714-0.002-0.01360.0173-0.02280.0422-2.1260.78812.4985
20.44780.1589-0.17050.423-0.21110.5896-0.0071-0.0917-0.0985-0.078-0.0555-0.03270.00220.04320.06270.02010.0112-0.0020.0340.02630.0433.1059-20.28126.0009
30.37250.3508-0.06080.8888-0.14520.1179-0.0195-0.0575-0.0638-0.1381-0.0411-0.03910.02770.03040.06060.03210.017-0.00190.04880.01190.041927.88118.339112.9227
40.39370.05380.00430.2020.30540.57560.0102-0.05130.0975-0.0252-0.04060.0167-0.018-0.00940.03040.01340.0212-0.00320.0458-0.02080.05725.967140.716824.1071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A129 - 318
2X-RAY DIFFRACTION2A319 - 482
3X-RAY DIFFRACTION3B129 - 298
4X-RAY DIFFRACTION4B299 - 482

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