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- PDB-7zhq: Crystal structure of TTBK1 in complex with compound 10 (7-009) -

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Basic information

Entry
Database: PDB / ID: 7zhq
TitleCrystal structure of TTBK1 in complex with compound 10 (7-009)
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-IRD / 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)36,51512
Polymers35,5151
Non-polymers1,00011
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint23 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.308, 39.543, 49.650
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.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IRD / (3~{S})-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-methyl-pent-1-yn-3-ol


Mass: 346.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
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→48.33 Å / Num. obs: 30388 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Net I/σ(I): 13.4 / Num. measured all: 203072
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.866.40.8581891929610.8290.3640.9342100
6.97-48.336.50.03437095720.9990.0140.03744.199.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q8W

7q8w


Resolution: 1.8→48.33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1988 / WRfactor Rwork: 0.1625 / FOM work R set: 0.8451 / SU B: 5.483 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1217 / SU Rfree: 0.1177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 1493 4.9 %RANDOM
Rwork0.1738 ---
obs0.1757 28895 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.3 Å2 / Biso mean: 25.998 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-0.21 Å2
2--2.11 Å20 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.8→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 67 183 2635
Biso mean--32.35 31.43 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172468
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.6543397
X-RAY DIFFRACTIONr_angle_other_deg1.3681.5975668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64420.903144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64915470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8021523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 111 -
Rwork0.254 2099 -
all-2210 -
obs--100 %
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)
13.67910.8403-0.08282.6938-0.1061.79350.0914-0.27070.28270.1615-0.04930.1635-0.1541-0.0692-0.04210.06050.01120.00260.1368-0.01730.030671.267439.14419.9181
22.04790.3296-0.08460.94360.07651.58520.00230.2145-0.0912-0.10520.02390.01160.02430.0647-0.02630.01330.0041-0.00450.0409-0.01950.009959.921831.2818-11.1397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 101
2X-RAY DIFFRACTION2A102 - 313

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