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- PDB-6u0k: TTBK2 kinase domain in complex with Compound 1 -

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Basic information

Entry
Database: PDB / ID: 6u0k
TitleTTBK2 kinase domain in complex with Compound 1
ComponentsTau-tubulin kinase 2
KeywordsTRANSFERASE / TTBK2
Function / homology
Function and homology information


negative regulation of microtubule binding / negative regulation of protein localization to microtubule / cerebellar granular layer development / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / smoothened signaling pathway / tau-protein kinase activity / kinesin binding ...negative regulation of microtubule binding / negative regulation of protein localization to microtubule / cerebellar granular layer development / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / smoothened signaling pathway / tau-protein kinase activity / kinesin binding / cilium assembly / regulation of cell migration / Anchoring of the basal body to the plasma membrane / centriole / cerebellum development / ciliary basal body / tau protein binding / microtubule cytoskeleton organization / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / extracellular space / ATP binding / nucleus / cytosol
Similarity search - Function
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE / PHOSPHATE ION / Tau-tubulin kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.744 Å
AuthorsMarcotte, D.J. / Chodaparambil, J.V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: The crystal structure of the catalytic domain of tau tubulin kinase 2 in complex with a small-molecule inhibitor
Authors: Marcotte, D.J. / Spilker, K.A. / Wen, D. / Hesson, T. / Patterson, T.A. / Kumar, R. / Chodaparambil, J.V.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Tau-tubulin kinase 2
A: Tau-tubulin kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,44614
Polymers68,9072
Non-polymers1,53912
Water7,566420
1
B: Tau-tubulin kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1286
Polymers34,4541
Non-polymers6745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Tau-tubulin kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3188
Polymers34,4541
Non-polymers8647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.230, 114.680, 118.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 14 or resid 16...
21(chain B and (resid 8 through 14 or resid 16...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 8 through 14 or resid 16...A8 - 14
121(chain A and (resid 8 through 14 or resid 16...A16 - 102
131(chain A and (resid 8 through 14 or resid 16...A104 - 105
141(chain A and (resid 8 through 14 or resid 16...A106
151(chain A and (resid 8 through 14 or resid 16...A8 - 901
161(chain A and (resid 8 through 14 or resid 16...A8 - 901
171(chain A and (resid 8 through 14 or resid 16...A8 - 901
181(chain A and (resid 8 through 14 or resid 16...A8 - 901
191(chain A and (resid 8 through 14 or resid 16...A8 - 901
211(chain B and (resid 8 through 14 or resid 16...B8 - 14
221(chain B and (resid 8 through 14 or resid 16...B16 - 17
231(chain B and (resid 8 through 14 or resid 16...B8 - 601
241(chain B and (resid 8 through 14 or resid 16...B8 - 601
251(chain B and (resid 8 through 14 or resid 16...B8 - 601
261(chain B and (resid 8 through 14 or resid 16...B8 - 601
271(chain B and (resid 8 through 14 or resid 16...B8 - 601
281(chain B and (resid 8 through 14 or resid 16...B8 - 601

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Components

#1: Protein Tau-tubulin kinase 2


Mass: 34453.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTBK2, KIAA0847 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6IQ55, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-DTQ / 4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE


Mass: 297.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2M Sodium Potassium Phosphate and 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 147854 / % possible obs: 97.9 % / Redundancy: 6.6 % / CC1/2: 0.99 / Net I/σ(I): 16.75
Reflection shellResolution: 1.74→1.84 Å / Num. unique obs: 23350 / CC1/2: 0.46 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BTK

4btk


Resolution: 1.744→46.46 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 3888 5 %
Rwork0.1909 73866 -
obs0.193 77754 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.36 Å2 / Biso mean: 40.546 Å2 / Biso min: 18.34 Å2
Refinement stepCycle: final / Resolution: 1.744→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4573 0 96 420 5089
Biso mean--66.26 46.91 -
Num. residues----582
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1686X-RAY DIFFRACTION7.093TORSIONAL
12B1686X-RAY DIFFRACTION7.093TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7441-1.76540.42811200.3699227986
1.7654-1.78770.31791380.31742620100
1.7877-1.81130.34371380.3029261198
1.8113-1.83610.36431360.2904260899
1.8361-1.86230.33041360.2697259298
1.8623-1.89010.27141360.2639257797
1.8901-1.91960.31131390.26142647100
1.9196-1.95110.32881370.2577260398
1.9511-1.98480.31481400.25482655100
1.9848-2.02080.27361390.226263199
2.0208-2.05970.27571380.21942635100
2.0597-2.10180.2461390.2263199
2.1018-2.14750.25791400.19852659100
2.1475-2.19740.27441380.2015262199
2.1974-2.25240.24291390.1952265399
2.2524-2.31330.22761390.19162643100
2.3133-2.38130.24151400.18792659100
2.3813-2.45820.21591410.20232678100
2.4582-2.5460.28571410.20652666100
2.546-2.6480.21711340.2124255596
2.648-2.76850.28751410.2074267199
2.7685-2.91440.23391410.19882679100
2.9144-3.0970.23441420.20222700100
3.097-3.3360.27841410.1952688100
3.336-3.67160.20221420.1713269399
3.6716-4.20260.20151420.1582268999
4.2026-5.29360.1811380.1456263295
5.2936-100.20461530.18282891100
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)
12.07171.671-0.02362.33590.22011.6167-0.14030.24470.0008-0.33090.12040.0117-0.4060.1693-0.00060.3359-0.0279-0.06570.25930.06270.247116.465512.6858-2.4262
21.6238-0.571-1.05098.56957.0546.86540.0720.3136-0.0948-0.472-0.17310.043-0.3388-0.35740.14990.285-0.0135-0.07470.29580.04910.237810.27153.4221-6.0276
32.25720.0783-0.37721.9590.13132.5902-0.0646-0.0744-0.40820.1259-0.0904-0.04320.19830.06570.15040.204-0.0206-0.02430.21010.06360.31098.9325-6.41647.3096
45.7999-0.60712.29192.3076-0.12953.5868-0.1995-0.27960.3947-0.28560.02670.258-0.5654-0.21680.16540.4760.0298-0.00440.2210.05680.345720.949437.204413.53
53.1011-0.51010.92161.92631.07773.3120.0574-0.03940.1331-0.2669-0.00380.1049-0.11140.168-0.02920.2097-0.0490.01480.1992-0.00140.182331.016327.383725.7576
63.5677-1.23920.24362.5620.18081.65630.0686-0.4494-0.04940.06180.0680.06250.04350.0382-0.1170.1898-0.0369-0.01690.2533-0.00920.160933.177721.336436.6503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 8 through 149 )B8 - 149
2X-RAY DIFFRACTION2chain 'B' and (resid 150 through 186 )B150 - 186
3X-RAY DIFFRACTION3chain 'B' and (resid 187 through 299 )B187 - 299
4X-RAY DIFFRACTION4chain 'A' and (resid 8 through 95 )A8 - 95
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 186 )A96 - 186
6X-RAY DIFFRACTION6chain 'A' and (resid 187 through 298 )A187 - 298

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