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- PDB-9hhw: Crystal structure of TTBK1 with a covalent compound GCL95 -

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Basic information

Entry
Database: PDB / ID: 9hhw
TitleCrystal structure of TTBK1 with a covalent compound GCL95
ComponentsTau-tubulin kinase 1
KeywordsTRANSFERASE / Kinase / Covalent / inhibitor / TTBK1
Function / homology
Function and homology information


positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation ...positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / substantia nigra development / peptidyl-threonine phosphorylation / peptidyl-tyrosine phosphorylation / tau protein binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / learning or memory / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tau-tubulin kinase 1, catalytic domain / : / 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
: / Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, G. / Seidler, N. / Gehringer, M. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Probing the Protein Kinases' Cysteinome by Covalent Fragments.
Authors: Wang, G. / Seidler, N.J. / Rohm, S. / Pan, Y. / Liang, X.J. / Haarer, L. / Berger, B.T. / Sivashanmugam, S.A. / Wydra, V.R. / Forster, M. / Laufer, S.A. / Chaikuad, A. / Gehringer, M. / Knapp, S.
History
DepositionNov 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tau-tubulin kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7802
Polymers35,5151
Non-polymers2651
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.641, 39.954, 166.667
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Tau-tubulin kinase 1 / Brain-derived tau kinase


Mass: 35515.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTBK1, BDTK, KIAA1855 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1IU7 / ~{N}-[2-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)phenyl]propanamide


Mass: 265.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 17% PEG 3350, 0.2 M sodium acetate pH 7.0 and 0.1 M tris pH 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999995 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 3→48.26 Å / Num. obs: 6759 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.977 / Net I/σ(I): 6
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1077 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.26 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.808 / SU B: 25.236 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.537 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28592 332 4.9 %RANDOM
Rwork0.23162 ---
obs0.23429 6426 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.71 Å2
Baniso -1Baniso -2Baniso -3
1--7.24 Å2-0 Å2-0.2 Å2
2--1.68 Å2-0 Å2
3---5.54 Å2
Refinement stepCycle: 1 / Resolution: 3→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 20 18 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122470
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162385
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.8573324
X-RAY DIFFRACTIONr_angle_other_deg0.5511.7855477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3095298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.7546.73126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72810460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022934
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02611
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_it2.723.4911177
X-RAY DIFFRACTIONr_mcbond_other2.7193.4911177
X-RAY DIFFRACTIONr_mcangle_it4.6436.2621471
X-RAY DIFFRACTIONr_mcangle_other4.6416.2661472
X-RAY DIFFRACTIONr_scbond_it2.6453.8581293
X-RAY DIFFRACTIONr_scbond_other2.6443.8631294
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6596.951851
X-RAY DIFFRACTIONr_long_range_B_refined10.67141.7510329
X-RAY DIFFRACTIONr_long_range_B_other10.6741.7510330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 22 -
Rwork0.339 482 -
obs--100 %

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