5ep6

The crystal structure of NAP1 in complex with TBK1

Method: X-RAY DIFFRACTION D_max: 66.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

5-azacytidine-induced protein 2

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 215–255	Fragment：UNP RESIDUES 215-255	Serine/threonine-protein kinase TBK1 × 1 （Q9UHD2） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 215–255	Fragment：UNP RESIDUES 215-255	Serine/threonine-protein kinase TBK1 × 1 （Q9UHD2） 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

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 5EP6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5Z7G Crystal structure of TAX1BP1 SKICH region in complex with NAP1 Deposited 2018-01-28	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 C 33–75（43 aa） Chain D 33–75（43 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；PEG 8000, 0.1 M HEPES	Resolution 2.30 Å R-free 0.233
5Z7L Crystal structure of NDP52 SKICH region in complex with NAP1 Deposited 2018-01-29	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 33–75（43 aa） Fragment：UNP residues 33-75 Chain D 33–75（43 aa） Fragment：UNP residues 33-75	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG3350,sodium malonate	Resolution 2.02 Å R-free 0.222
7EA2 crystal structure of NAP1 FIR in complex with RB1CC1 Claw domain Deposited 2021-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 6–16（11 aa） Chain B 6–16（11 aa）	Not recorded	P6G HEXAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M phosphate/citrate pH 4.2, 40% PEG300	Resolution 2.14 Å R-free 0.232

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AZI2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–41； UniProt 215–255 Author chain C； PDBConstruct 1–41； UniProt 215–255

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 677–729	Fragment：UNP RESIDUES 677-729	5-azacytidine-induced protein 2 × 1 （Q9H6S1） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 677–729	Fragment：UNP RESIDUES 677-729	5-azacytidine-induced protein 2 × 1 （Q9H6S1） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5EP6	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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
4IW0 Crystal structure and mechanism of activation of TBK1 Deposited 2013-01-23	Different construct Different mutation/modification Different oligomeric state 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：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
4IWO Crystal structure and mechanism of activation of TBK1 Deposited 2013-01-24	Different construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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	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 construct Different mutation/modification Different oligomeric state 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 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 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
5W5V TBK1 co-crystal structure with amlexanox Deposited 2017-06-15	Different construct Different oligomeric state 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 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 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 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 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 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 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 ligand/ion 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 construct Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct 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 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TBK1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–58； UniProt 677–729 Author chain D； PDBConstruct 6–58； UniProt 677–729

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ep6
Deposition date deposition_date	2015-11-11
Structure title title	The crystal structure of NAP1 in complex with TBK1
Keywords keywords	NAP1, TBK1, CALCOCO2, PROTEIN BINDING-TRANSFERASE complex; PROTEIN BINDING/TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.40 Å
Radius of gyration Rg (electron density) rg_electron	18.65 Å
Forward intensity I(0) i0	7130480.00
Molecular weight molecular_weight	19105.0 kDa
Excluded volume excluded_volume	23807 Å³
Envelope volume envelope_volume	28476 Å³
Hydration-shell volume shell_volume	13882 Å³
Envelope diameter envelope_diameter	64.9 Å
Shell Rg shell_rg	23.25 Å
Envelope Rg envelope_rg	19.17 Å
Shape Rg shape_rg	18.63 Å
Total Rg total_rg	19.46 Å
Total atoms total_atoms	1329
Residues n_residues	163
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.3 Å
Rg (real space) rg_real	19.61 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	7.1300e+06
I(0) uncertainty (real space) i0_real_error	9.0170e+04
Rg (reciprocal space) rg_reciprocal	19.58 Å
I(0) (reciprocal space) i0_reciprocal	7130000.0000
Solution quality estimate total_estimate	0.7979
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.581
Kurtosis Kurtosis kurtosis	-0.250
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3466000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.615; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.688; Smooth: 0.838

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	5-azacytidine-induced protein 2
Molecular weight formula_weight	5631.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1599

SSDNMQHAYWELKREMSNLHLVTQVQAELLRKLKTSTAIKKENLYFQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein kinase TBK1
Molecular weight formula_weight	6324.2 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SGSGSYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMDGGLRNVDCL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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8. Citations (1)

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Unit-cell length a length_a	41.360 Å
Unit-cell length b length_b	50.113 Å
Unit-cell length c length_c	84.416 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.451 Å
Low-resolution limit resolution_low	43.092 Å
R factor r_factor	0.1883
R_work r_work	0.1867
R_free r_free	0.2174

fit	/app/data/saxs_computation/ep/5ep6/5ep6.fit
pddf	/app/data/pr_computation/ep/5ep6/5ep6.pr.out
profile	/app/data/saxs_computation/ep/5ep6/5ep6.dat

The crystal structure of NAP1 in complex with TBK1

1. Protein Identity and Related Structures Protein Identity & Related Structures

5-azacytidine-induced protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein kinase TBK1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)