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4iw0

Crystal structure and mechanism of activation of TBK1

Method: X-RAY DIFFRACTION Dmax: 131.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein kinase TBK1

Homo sapiens

UniProt Q9UHD2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–657 Mutation：D135N Non-standard monomer：Yes (specific site not provided by mmCIF) BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；5% PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 4.00 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4IW0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4EFO Crystal structure of the ubiquitin-like domain of human TBK1 Deposited 2012-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 302–383（82 aa） Fragment：ubiquitin-like domain, UNP RESIDUE 302-383
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；289 K；0.1M BIS-TRIS,0.2M NaCl,21% PEG 3350, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.77 Å R-free 0.204
4EFO Crystal structure of the ubiquitin-like domain of human TBK1 Deposited 2012-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 302–383（82 aa） Fragment：ubiquitin-like domain, UNP RESIDUE 302-383
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；289 K；0.1M BIS-TRIS,0.2M NaCl,21% PEG 3350, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 1.77 Å R-free 0.204
4EUT Structure of BX-795 Complexed with Unphosphorylated Human TBK1 Kinase-ULD Domain Deposited 2012-04-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–385（384 aa） Fragment：Kinase-ULD Domain, UNP residues 2-385
Chain B 2–385（384 aa） Fragment：Kinase-ULD Domain, UNP residues 2-385
Mutation：D135N Mutation：D135N BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 2 IOD IODIDE ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M lithium sulfate, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.257
4EUU Structure of BX-795 Complexed with Human TBK1 Kinase Domain Phosphorylated on Ser172 Deposited 2012-04-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–308（307 aa） Fragment：Kinase Domain, UNP residues 2-308
Chain B 2–308（307 aa） Fragment：Kinase Domain, UNP residues 2-308
Mutation：D135N Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D135N Non-standard monomer：Yes (specific site not provided by mmCIF) BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 2 IOD IODIDE ION × 2 SO4 SULFATE ION × 3 GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M BIS-TRIS pH 5.5 (5.5-7.5), 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.194
4IM0 Structure of Tank-Binding Kinase 1 Deposited 2013-01-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–657（657 aa） Fragment：residues 1 to 657
Mutation：D135N 1FV N-{3-[(5-cyclopropyl-2-{[3-(morpholin-4-ylmethyl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；4% (w/v) PEG8000, 100 mM Tris pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.236
4IM2 Structure of Tank-Binding Kinase 1 Deposited 2013-01-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–657（657 aa） Fragment：residues 1 to 657
Mutation：D135N BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；4% (w/v) PEG8000, 100 mM Tris pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.255
4IM2 Structure of Tank-Binding Kinase 1 Deposited 2013-01-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–657（657 aa） Fragment：residues 1 to 657
Mutation：D135N BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；4% (w/v) PEG8000, 100 mM Tris pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.255
4IM3 Structure of Tank-Binding Kinase 1 Deposited 2013-01-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–657（657 aa） Fragment：residues 1 to 657
Mutation：D135N BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 2 HG MERCURY (II) ION × 10 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；4% MPD, 100 mM Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.34 Å R-free 0.279
4IWO Crystal structure and mechanism of activation of TBK1 Deposited 2013-01-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–657（656 aa）
Mutation：S172A 1H4 N-{3-[(5-cyclopropyl-2-{[3-(2-oxopyrrolidin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；5% PEG6000, pH 7.5, vapor diffusion, hanging drop, temperature 294K
Resolution 2.61 Å R-free 0.263
4IWP Crystal structure and mechanism of activation of TBK1 Deposited 2013-01-24 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–657（656 aa）
Mutation：S172A BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；5% PEG6000, pH 7.5, vapor diffusion, hanging drop, temperature 294K
Resolution 3.06 Å R-free 0.335
4IWQ Crystal structure and mechanism of activation of TBK1 Deposited 2013-01-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–657（656 aa）
Mutation：S172A 1FV N-{3-[(5-cyclopropyl-2-{[3-(morpholin-4-ylmethyl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；5% PEG6000, pH 7.5, vapor diffusion, hanging drop, temperature 294K
Resolution 3.00 Å R-free 0.310
4IWQ Crystal structure and mechanism of activation of TBK1 Deposited 2013-01-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–657（656 aa）
Mutation：S172A 1FV N-{3-[(5-cyclopropyl-2-{[3-(morpholin-4-ylmethyl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；5% PEG6000, pH 7.5, vapor diffusion, hanging drop, temperature 294K
Resolution 3.00 Å R-free 0.310
5EOA Crystal structure of OPTN E50K mutant and TBK1 complex Deposited 2015-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 677–729（53 aa） Fragment：UNP RESIDUES 677-729
Chain D 677–729（53 aa） Fragment：UNP RESIDUES 677-729
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6；291.5 K；0.1M MES monohydrate pH 6.0, 14% w/V Polyethylene glycol 4000
Resolution 2.50 Å R-free 0.267
5EOF Crystal structure of OPTN NTD and TBK1 CTD complex Deposited 2015-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 677–729（53 aa） Fragment：UNP RESIDUES 677-729
Chain D 677–729（53 aa） Fragment：UNP RESIDUES 677-729
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291.15 K；0.1M MES monohydrate pH 6.0, 14% w/v polyethylene glycol 4000
Resolution 2.05 Å R-free 0.245
5EP6 The crystal structure of NAP1 in complex with TBK1 Deposited 2015-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 677–729（53 aa） Fragment：UNP RESIDUES 677-729
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；1% w/v Tryptone, 0.05 M HEPES sodium (pH 7.0), 12% w/v PEG 3350
Resolution 1.45 Å R-free 0.217
5EP6 The crystal structure of NAP1 in complex with TBK1 Deposited 2015-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 677–729（53 aa） Fragment：UNP RESIDUES 677-729
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；1% w/v Tryptone, 0.05 M HEPES sodium (pH 7.0), 12% w/v PEG 3350
Resolution 1.45 Å R-free 0.217
5W5V TBK1 co-crystal structure with amlexanox Deposited 2017-06-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–657（657 aa）
Not recorded ANW 2-amino-7-(1-methylethyl)-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES pH 7.5, 4% PEG 8000, 10% DMSO
Resolution 3.65 Å R-free 0.290
6BNY TBK1 in complex with tetrazole analog of amlexanox Deposited 2017-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–657（657 aa）
Not recorded E0M 2-amino-7-(propan-2-yl)-3-(1H-tetrazol-5-yl)-5H-[1]benzopyrano[2,3-b]pyridin-5-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 4% PEG 8000
Resolution 3.34 Å R-free 0.287
6BOD TBK1 in complex with ethyl ester analog of amlexanox Deposited 2017-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–657（657 aa）
Not recorded E0P ethyl 2-amino-5-oxo-7-(propan-2-yl)-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 4% PEG 8000
Resolution 3.20 Å R-free 0.271
6BOE TBK1 in complex with amide-coupled tetrazole analog of amlexanox Deposited 2017-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–657（657 aa）
Not recorded E0S 2-amino-5-oxo-7-(propan-2-yl)-N-(1H-tetrazol-5-yl)-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 5% PEG 8000
Resolution 3.60 Å R-free 0.291
6CQ0 TBK1 in Complex with Dimethyl Amino Analog of Amlexanox Deposited 2018-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–657（657 aa）
Not recorded F8M 2-amino-7-[3-(dimethylamino)propyl]-5-oxo-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 4% PEG 8000, 10% DMSO
Resolution 3.19 Å R-free 0.293
6CQ4 TBK1 in Complex with Cyclohexyl Analog of Amlexanox Deposited 2018-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–657（657 aa）
Not recorded F8P 2-amino-7-(4,4-difluorocyclohexyl)-5-oxo-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 4% PEG 8000, 10% DMSO
Resolution 3.20 Å R-free 0.272
6CQ5 TBK1 in Complex with Sulfone Analog of Amlexanox Deposited 2018-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–657（657 aa）
Not recorded F8S 2-amino-7-(1,1-dioxo-1lambda~6~-thian-4-yl)-5-oxo-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 4% PEG 8000, 10% DMSO
Resolution 3.35 Å R-free 0.275
6NT9 Cryo-EM structure of the complex between human TBK1 and chicken STING Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–729（729 aa）
Chain B 1–729（729 aa）
Mutation：D135N Mutation：D135N No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6O8B Crystal structure of STING CTD in complex with TBK1 Deposited 2019-03-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–657（656 aa）
Chain B 2–657（656 aa）
Mutation：D135N, S172E Mutation：D135N, S172E BX7 N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.8 M (NH4)2SO4, 0.1 M BIS-TRIS pH 5.5 and 1% PEG3350
Resolution 3.40 Å R-free 0.258
6RSR TBK1 in complex with compound 2 Deposited 2019-05-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–657（656 aa）
Not recorded KHT ~{N}-(cyclopropen-1-ylmethyl)-2-[[4-[[4-[3,3,3-tris(fluoranyl)propanoyl]piperazin-1-yl]methyl]pyridin-2-yl]amino]-1~{H}-benzimidazole-5-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；100 mM HEPES pH 7.5, 5-8% PEG 8000
Resolution 3.15 Å R-free 0.307
6RST TBK1 in complex with inhibitor compound 24 Deposited 2019-05-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–657（656 aa）
Mutation：S172E KHQ 1-[4-[(1~{R})-1-[2-[[5-[1-(cyclopropylmethyl)pyrazol-4-yl]-1~{H}-benzimidazol-2-yl]amino]pyridin-4-yl]ethyl]piperazin-1-yl]-3,3,3-tris(fluoranyl)propan-1-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；100 mM HEPES pH 7.5 and 5-8% PEG 8000
Resolution 3.29 Å R-free 0.303
6RSU TBK1 in complex with Inhibitor compound 35 Deposited 2019-05-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–657（656 aa）
Not recorded KJB 3,3,3-tris(fluoranyl)-1-[4-[(1~{R})-1-[2-[[(2~{S})-5-(5-propan-2-yloxypyrimidin-4-yl)-2,3-dihydro-1~{H}-benzimidazol-2-yl]amino]pyridin-4-yl]ethyl]piperazin-1-yl]propan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100 mM HEPES pH 7.5, 5-8% PEG 8000
Resolution 2.75 Å R-free 0.351

24 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–658； UniProt 2–657

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4iw0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4iw0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4iw0
Deposition date deposition_date2013-01-23
Structure title titleCrystal structure and mechanism of activation of TBK1
Keywords keywordsKINASE, ATP binding, Phosphorylation, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.45 Å
Radius of gyration Rg (electron density) rg_electron34.64 Å
Forward intensity I(0) i088457300.00
Molecular weight molecular_weight75196.0 kDa
Excluded volume excluded_volume94355 ų
Envelope volume envelope_volume126670 ų
Hydration-shell volume shell_volume33606 ų
Envelope diameter envelope_diameter137.2 Å
Shell Rg shell_rg36.88 Å
Envelope Rg envelope_rg35.61 Å
Shape Rg shape_rg34.63 Å
Total Rg total_rg34.84 Å
Total atoms total_atoms5287
Residues n_residues647
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax131.3 Å
Rg (real space) rg_real34.95 Å
Rg uncertainty (real space) rg_real_error1.90 Å
I(0) (real space) i0_real8.8460e+07
I(0) uncertainty (real space) i0_real_error1.5960e+06
Rg (reciprocal space) rg_reciprocal34.64 Å
I(0) (reciprocal space) i0_reciprocal88430000.0000
Solution quality estimate total_estimate0.7693
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3 Å
Skewness Skewness skewness0.768
Kurtosis Kurtosis kurtosis0.248
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10250000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.480; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.638; Smooth: 0.919
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4iw0A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id4iw0A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4iw0A03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4iw0A04
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily420 —
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8. Citations (1)

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9. Files and Curves (10)