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- PDB-7zhp: Crystal structure of TTBK1 in complex with compound 9 (7-005) -

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Basic information

Entry
Database: PDB / ID: 7zhp
TitleCrystal structure of TTBK1 in complex with compound 9 (7-005)
ComponentsTau-tubulin kinase 1
KeywordsTRANSFERASE / kinase / ttbk1 / tau tubulin kinase 1 / inhibitor complex
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 / peptidyl-threonine phosphorylation / substantia nigra development / peptidyl-tyrosine phosphorylation / peptidyl-serine phosphorylation / tau protein binding ...positive regulation of astrocyte activation / positive regulation of microglial cell activation / microtubule associated complex / tau-protein kinase activity / positive regulation of protein polymerization / peptidyl-threonine phosphorylation / substantia nigra development / peptidyl-tyrosine phosphorylation / peptidyl-serine phosphorylation / tau protein binding / protein tyrosine kinase activity / learning or memory / non-specific serine/threonine protein kinase / negative regulation of gene expression / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / 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 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Tau-tubulin kinase 1, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Chem-IQY / PHOSPHATE ION / Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChaikuad, A. / Axtman, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis.
Authors: Bashore, F.M. / Marquez, A.B. / Chaikuad, A. / Howell, S. / Dunn, A.S. / Beltran, A.A. / Smith, J.L. / Drewry, D.H. / Beltran, A.S. / Axtman, A.D.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)36,3439
Polymers35,5151
Non-polymers8288
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint12 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.288, 39.793, 49.791
Angle α, β, γ (deg.)90.000, 103.230, 90.000
Int Tables number5
Space group name H-MC121

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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 / Plasmid: pSumo-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IQY / 1-(4-azanyl-3,5,12-triazatetracyclo[9.7.0.0^{2,7}.0^{13,18}]octadeca-1(11),2,4,6,13(18),14,16-heptaen-16-yl)-3-ethyl-pent-1-yn-3-ol


Mass: 360.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 14-23% PEG 3350, 0.2 M sodium acetate pH 7.0 and 0.1 M tris pH 7.5-9.0
PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.8→48.47 Å / Num. obs: 30838 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.866.80.852229920.8170.3871.017100
6.97-48.476.50.02658210.0110.02899.8

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7q8w

7q8w


Resolution: 1.8→48.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.607 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1522 4.9 %RANDOM
Rwork0.1765 ---
obs0.1786 29315 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.28 Å2 / Biso mean: 31.494 Å2 / Biso min: 9.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0.01 Å2
2--2.26 Å20 Å2
3----1.58 Å2
Refinement stepCycle: final / Resolution: 1.8→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 56 209 2650
Biso mean--35.07 38.17 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132506
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172434
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.6483363
X-RAY DIFFRACTIONr_angle_other_deg1.3181.5995587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6815298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27921.056142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5121522
X-RAY DIFFRACTIONr_chiral_restr0.070.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022886
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02614
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 116 -
Rwork0.276 2144 -
all-2260 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 63.3603 Å / Origin y: 33.4307 Å / Origin z: -5.4054 Å
111213212223313233
T0.0041 Å20.0092 Å2-0.0069 Å2-0.0505 Å2-0.0212 Å2--0.0267 Å2
L2.5277 °20.454 °20.3559 °2-0.8697 °2-0.0486 °2--1.2874 °2
S0.0068 Å °0.0498 Å °-0.027 Å °-0.0183 Å °0.0049 Å °0.0219 Å °-0.0279 Å °0.0838 Å °-0.0117 Å °

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