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- PDB-4btj: TTBK1 in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 4btj
TitleTTBK1 in complex with ATP
ComponentsTAU-TUBULIN KINASE 1
KeywordsTRANSFERASE / LIGAND COMPLEX / STRUCTURE-KINETICS RELATIONSHIP
Function / homology
Function and homology information


positive regulation of astrocyte activation / positive regulation of cyclin-dependent protein kinase activity / positive regulation of microglial cell activation / positive regulation of cysteine-type endopeptidase activity / microtubule associated complex / positive regulation of protein polymerization / tau-protein kinase activity / substantia nigra development / negative regulation of protein binding / peptidyl-threonine phosphorylation ...positive regulation of astrocyte activation / positive regulation of cyclin-dependent protein kinase activity / positive regulation of microglial cell activation / positive regulation of cysteine-type endopeptidase activity / microtubule associated complex / positive regulation of protein polymerization / tau-protein kinase activity / substantia nigra development / negative regulation of protein binding / peptidyl-threonine phosphorylation / tau protein binding / peptidyl-tyrosine phosphorylation / peptidyl-serine phosphorylation / protein tyrosine kinase activity / learning or memory / non-specific serine/threonine protein kinase / protein phosphorylation / 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
Similarity search - Function
Tau-tubulin kinase 1, catalytic domain / 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. ...Tau-tubulin kinase 1, catalytic domain / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsXue, Y. / Wan, P. / Hillertz, P. / Schweikart, F. / Zhao, Y. / Wissler, L. / Dekker, N.
CitationJournal: Chemmedchem / Year: 2013
Title: X-Ray Structural Analysis of Tau-Tubulin Kinase 1 and its Interactions with Small Molecular Inhibitors.
Authors: Xue, Y. / Wan, P.T. / Hillertz, P. / Schweikart, F. / Zhao, Y. / Wissler, L. / Dekker, N.
History
DepositionJun 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Mar 29, 2017Group: Source and taxonomy
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAU-TUBULIN KINASE 1
B: TAU-TUBULIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8078
Polymers77,4932
Non-polymers1,3146
Water11,115617
1
A: TAU-TUBULIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4595
Polymers38,7471
Non-polymers7124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TAU-TUBULIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3493
Polymers38,7471
Non-polymers6022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.980, 110.020, 110.550
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TAU-TUBULIN KINASE 1 / BRAIN-DERIVED TAU KINASE


Mass: 38746.543 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 1-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase, tau-protein kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.93 Å3/Da / Density % sol: 78.8 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.16→21.77 Å / Num. obs: 79065 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 36.67 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.3
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / % possible all: 87.3

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→21.77 Å / Cor.coef. Fo:Fc: 0.9461 / Cor.coef. Fo:Fc free: 0.9366 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 3969 5.03 %RANDOM
Rwork0.1784 ---
obs0.1794 78982 98.04 %-
Displacement parametersBiso mean: 39.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.2796 Å20 Å2-0.5071 Å2
2---3.7274 Å20 Å2
3---4.0071 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: LAST / Resolution: 2.16→21.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 78 617 5460
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014947HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046662HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1809SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes709HARMONIC5
X-RAY DIFFRACTIONt_it4947HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion18.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion599SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5942SEMIHARMONIC4
LS refinement shellResolution: 2.16→2.22 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 264 5.06 %
Rwork0.2125 4955 -
all0.2126 5219 -
obs--98.04 %

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