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- PDB-4btm: TTBK1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4btm
TitleTTBK1 in complex with inhibitor
ComponentsTAU-TUBULIN KINASE 1
KeywordsTRANSFERASE / LIGAND COMPLEX / STRUCTURE-KINETICS RELATIONSHIP
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-F8E / Tau-tubulin kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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: Derived calculations / Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)78,74210
Polymers77,4932
Non-polymers1,2498
Water6,467359
1
A: TAU-TUBULIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3825
Polymers38,7471
Non-polymers6354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TAU-TUBULIN KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3605
Polymers38,7471
Non-polymers6134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.590, 108.420, 110.760
Angle α, β, γ (deg.)90.00, 94.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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
Details: KINASE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase, tau-protein kinase

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Non-polymers , 5 types, 367 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-F8E / methyl 2-bromo-5-(7H-pyrrolo[2,3-d]pyrimidin-4-ylamino)benzoate


Mass: 347.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11BrN4O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 0.92
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.54→43.29 Å / Num. obs: 48993 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 68.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.54→2.61 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CKI, 1LHX, 2CMW, 2IZU, 2V62, 3GGF, 3OP5

1cki

1lhx

2cmw

2izu

2v62

3ggf

3op5


Resolution: 2.54→43.29 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.173
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 2477 5.06 %RANDOM
Rwork0.1773 ---
obs0.1789 48991 98.66 %-
Displacement parametersBiso mean: 56.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.5672 Å20 Å2-0.1069 Å2
2---6.3186 Å20 Å2
3---4.7514 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.54→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 72 359 5196
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014941HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116641HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1789SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes116HARMONIC2
X-RAY DIFFRACTIONt_gen_planes727HARMONIC5
X-RAY DIFFRACTIONt_it4941HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion19.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion591SEMIHARMONIC5
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_contact5531SEMIHARMONIC4
LS refinement shellResolution: 2.54→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2599 179 5.08 %
Rwork0.2265 3345 -
all0.2281 3524 -
obs--98.66 %

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