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- PDB-7zho: Crystal structure of TTBK1 in complex with compound 3 (7-001) -

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Basic information

Entry
Database: PDB / ID: 7zho
TitleCrystal structure of TTBK1 in complex with compound 3 (7-001)
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 / cytoplasm / cytosol
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-IQR / PHOSPHATE ION / Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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)36,1517
Polymers35,5151
Non-polymers6366
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint7 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.442, 49.424, 171.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IQR / 4-[3-(2-azanylpyrimidin-4-yl)-1~{H}-indol-5-yl]-2-methyl-but-3-yn-2-ol


Mass: 292.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
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: 2.08→47.48 Å / Num. obs: 20721 / % possible obs: 99 % / Redundancy: 11.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.045 / Rrim(I) all: 0.158 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.08-2.159.50.9982.119140.740.3431.11196.9
8.06-47.48110.0554380.9980.0170.05899.8

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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: 2.08→47.48 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.899 / SU B: 10.77 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1027 5 %RANDOM
Rwork0.1957 ---
obs0.1986 19643 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.03 Å2 / Biso mean: 34.753 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å2-0 Å2
2---0.94 Å20 Å2
3----0.92 Å2
Refinement stepCycle: final / Resolution: 2.08→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 43 151 2603
Biso mean--38.31 38.45 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132514
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172427
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.6443379
X-RAY DIFFRACTIONr_angle_other_deg1.2221.5945571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4935302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.521.056142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30515462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4211522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022914
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02618
LS refinement shellResolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 77 -
Rwork0.264 1374 -
all-1451 -
obs--97.38 %
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)
12.96-0.24951.09732.852-0.71964.72760.01960.03610.07010.0018-0.0264-0.3361-0.24590.48350.00680.2196-0.0029-0.00570.1308-0.07530.11186.042915.145330.214
21.3938-0.15170.15542.1177-0.70132.0592-0.003-0.0322-0.07060.06340.0124-0.08520.1968-0.0392-0.00940.0984-0.0279-0.00950.00980.00280.0084-1.9539-3.26313.8386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 108
2X-RAY DIFFRACTION2A109 - 317

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