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- PDB-4euu: Structure of BX-795 Complexed with Human TBK1 Kinase Domain Phosp... -

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Basic information

Entry
Database: PDB / ID: 4euu
TitleStructure of BX-795 Complexed with Human TBK1 Kinase Domain Phosphorylated on Ser172
ComponentsSerine/threonine-protein kinase TBK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / ATP Binding / Phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / serine/threonine protein kinase complex / dendritic cell proliferation / regulation of type I interferon production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / Interleukin-37 signaling / cGAS/STING signaling pathway ...IRF3 mediated activation of type 1 IFN / STAT6-mediated induction of chemokines / positive regulation of xenophagy / serine/threonine protein kinase complex / dendritic cell proliferation / regulation of type I interferon production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / Interleukin-37 signaling / cGAS/STING signaling pathway / TNFR1-induced proapoptotic signaling / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / positive regulation of interferon-alpha production / positive regulation of macroautophagy / positive regulation of type I interferon production / positive regulation of autophagy / canonical NF-kappaB signal transduction / antiviral innate immune response / negative regulation of TORC1 signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of TORC1 signaling / activation of innate immune response / positive regulation of interferon-beta production / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / Regulation of TNFR1 signaling / peptidyl-threonine phosphorylation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of peptidyl-serine phosphorylation / peptidyl-serine phosphorylation / TRAF3-dependent IRF activation pathway / positive regulation of canonical NF-kappaB signal transduction / protein phosphatase binding / Potential therapeutics for SARS / defense response to virus / nucleic acid binding / non-specific serine/threonine protein kinase / protein kinase activity / defense response to Gram-positive bacterium / inflammatory response / protein phosphorylation / negative regulation of gene expression / intracellular membrane-bounded organelle / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain ...TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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-BX7 / IODIDE ION / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMa, X. / Helgason, E. / Phung, Q.T. / Quan, C.L. / Iyer, R.S. / Lee, M.W. / Bowman, K.K. / Starovasnik, M.A. / Dueber, E.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis of Tank-binding kinase 1 activation by transautophosphorylation.
Authors: Ma, X. / Helgason, E. / Phung, Q.T. / Quan, C.L. / Iyer, R.S. / Lee, M.W. / Bowman, K.K. / Starovasnik, M.A. / Dueber, E.C.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase TBK1
B: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,72816
Polymers72,3582
Non-polymers2,37014
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-56 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.095, 76.095, 130.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 36178.988 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residues 2-308 / Mutation: D135N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBK1, NAK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UHD2, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 569 molecules

#2: Chemical ChemComp-BX7 / N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide


Mass: 591.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26IN7O2S
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE 5-IODO SUBSTITUTION OF THE PYRIMIDINE IN BX-795 IS SENSITIVE TO RADIATION CLEAVAGE. THE IONIZED ...THE 5-IODO SUBSTITUTION OF THE PYRIMIDINE IN BX-795 IS SENSITIVE TO RADIATION CLEAVAGE. THE IONIZED IODINE RADICALS DIFFUSE AWAY FROM ITS ORIGINAL POSITION. BOTH THE POSITIONS OF THE IODINE HAS BEEN CAPTURED AND REPRESENTED AS ALTERNATE CONFORMERS

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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: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5 (5.5-7.5), 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 7872 / Rsym value: 0.458 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.189 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19444 3948 5 %RANDOM
Rwork0.16855 ---
obs0.16988 74552 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.952 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20.56 Å20 Å2
2--1.11 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 127 555 5576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225125
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.986919
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99624.083240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04715.034872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1691532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213870
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5541.53052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44624924
X-RAY DIFFRACTIONr_scbond_it3.94532073
X-RAY DIFFRACTIONr_scangle_it5.7894.51995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 289 -
Rwork0.292 5548 -
obs--99.73 %
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)
10.9003-0.35360.49650.7772-0.29762.7660.02190.1153-0.15450.170.06120.13520.6815-0.34-0.0830.39450.00210.02320.25790.00320.1866-1.681-18.8569.659
23.2836-0.46490.30980.6945-0.17012.4312-0.1678-0.0539-0.27990.32890.18340.00520.6388-0.0761-0.01560.82740.1742-0.00060.09360.04160.187810.825-26.86125.969
30.4743-0.2108-0.26460.9770.32242.6771-0.03560.16010.05620.14130.0463-0.1331-0.00330.4255-0.01070.16880.0778-0.00690.42430.01350.196418.408-3.6750.036
41.83051.03070.24761.74240.72353.45940.10430.0966-0.2563-0.0378-0.1399-0.2430.78680.39940.03560.2510.24210.04270.6384-0.00910.190322.517-17.99-16.512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 221
2X-RAY DIFFRACTION2A222 - 307
3X-RAY DIFFRACTION3B0 - 219
4X-RAY DIFFRACTION4B220 - 307

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