1z0n

the glycogen-binding domain of the AMP-activated protein kinase

Method: X-RAY DIFFRACTION D_max: 81.9 Å Quality: GOOD

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

;5'-AMP-activated protein kinase, beta-1 subunit ;

Rattus norvegicus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 67–162	Fragment：68-163 fragment Mutation：L105M Non-standard monomer：Yes (specific site not provided by mmCIF)	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 1.49 Å R-free 0.213
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 67–162	Fragment：68-163 fragment Mutation：L105M Non-standard monomer：Yes (specific site not provided by mmCIF)	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 1.49 Å R-free 0.213
3	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 67–162	Fragment：68-163 fragment Mutation：L105M Non-standard monomer：Yes (specific site not provided by mmCIF)	Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 1.49 Å R-free 0.213

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 1Z0N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z0M the glycogen-binding domain of the AMP-activated protein kinase beta1 subunit Deposited 2005-03-02	Different construct Different mutation/modification Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 67–162（96 aa） Fragment：68-163 of beta1 subunit	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 1.91 Å R-free 0.243
1Z0M the glycogen-binding domain of the AMP-activated protein kinase beta1 subunit Deposited 2005-03-02	Different construct Different mutation/modification Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 67–162（96 aa） Fragment：68-163 of beta1 subunit	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 1.91 Å R-free 0.243
1Z0M the glycogen-binding domain of the AMP-activated protein kinase beta1 subunit Deposited 2005-03-02	Different construct Different mutation/modification Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 67–162（96 aa） Fragment：68-163 of beta1 subunit	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；299 K；PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K	Resolution 1.91 Å R-free 0.243
4EAG Co-crystal structure of an chimeric AMPK core with ATP Deposited 2012-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 187–270（84 aa） Fragment：UNP residues 187-270	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.02；298 K；MES, 12% Methanol, 2% 1,4-butanodiol, pH 6.02 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.252
4EAK Co-crystal structure of an AMPK core with ATP Deposited 2012-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 200–270（71 aa） Fragment：UNP residues 200-270	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；298 K；0.1M MES pH 5.9, 18% IPP, VAPOR DIFFUSION, HANGING DROP, temperature 298 K	Resolution 2.50 Å R-free 0.254
4EAL Co-crystal of AMPK core with ATP soaked with AMP Deposited 2012-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 200–270（71 aa） Fragment：UNP residues 200-270	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；298 K；0.1M MES pH5.9, 18% IPP, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.51 Å R-free 0.277
4QFG Structure of AMPK in complex with STAUROSPORINE inhibitor and in the absence of a synthetic activator Deposited 2014-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 67–269（203 aa） Fragment：AMPK beta1	Mutation：S108D	STU STAUROSPORINE × 1 CL CHLORIDE ION × 3 SO4 SULFATE ION × 3 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；750 mM Ammonium Sulfate, 500 mM Lithium Sulfate, 100 mM tri-Sodium Citrate, 1% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.46 Å R-free 0.267
4QFG Structure of AMPK in complex with STAUROSPORINE inhibitor and in the absence of a synthetic activator Deposited 2014-05-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 67–269（203 aa） Fragment：AMPK beta1	Mutation：S108D	STU STAUROSPORINE × 2 CL CHLORIDE ION × 6 SO4 SULFATE ION × 6 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；750 mM Ammonium Sulfate, 500 mM Lithium Sulfate, 100 mM tri-Sodium Citrate, 1% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.46 Å R-free 0.267
4QFR Structure of AMPK in complex with Cl-A769662 activator and STAUROSPORINE inhibitor Deposited 2014-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa） Fragment：AMPK beta 1	Mutation：S108D	STU STAUROSPORINE × 1 CL CHLORIDE ION × 5 32J 2-chloro-4-hydroxy-3-(2'-hydroxybiphenyl-4-yl)-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile × 1 AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；750 mM Ammonium Sulfate, 500 mM Lithium Sulfate, 100 mM tri-Sodium Citrate, 1% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.34 Å R-free 0.249
4QFR Structure of AMPK in complex with Cl-A769662 activator and STAUROSPORINE inhibitor Deposited 2014-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa） Fragment：AMPK beta 1	Mutation：S108D	STU STAUROSPORINE × 2 CL CHLORIDE ION × 10 32J 2-chloro-4-hydroxy-3-(2'-hydroxybiphenyl-4-yl)-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile × 2 AMP ADENOSINE MONOPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；750 mM Ammonium Sulfate, 500 mM Lithium Sulfate, 100 mM tri-Sodium Citrate, 1% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.34 Å R-free 0.249
4QFR Structure of AMPK in complex with Cl-A769662 activator and STAUROSPORINE inhibitor Deposited 2014-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa） Fragment：AMPK beta 1	Mutation：S108D	STU STAUROSPORINE × 2 CL CHLORIDE ION × 10 32J 2-chloro-4-hydroxy-3-(2'-hydroxybiphenyl-4-yl)-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile × 2 AMP ADENOSINE MONOPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；750 mM Ammonium Sulfate, 500 mM Lithium Sulfate, 100 mM tri-Sodium Citrate, 1% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.34 Å R-free 0.249
4QFS Structure of AMPK in complex with Br2-A769662core activator and STAUROSPORINE inhibitor Deposited 2014-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa） Fragment：AMPK beta 1	Mutation：S108D	STU STAUROSPORINE × 1 32H 2-bromo-3-(4-bromophenyl)-4-hydroxy-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile × 1 CL CHLORIDE ION × 5 AMP ADENOSINE MONOPHOSPHATE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；750 mM Ammonium Sulfate, 500 mM Lithium Sulfate, 100 mM tri-Sodium Citrate, 1% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.55 Å R-free 0.269
4QFS Structure of AMPK in complex with Br2-A769662core activator and STAUROSPORINE inhibitor Deposited 2014-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa） Fragment：AMPK beta 1	Mutation：S108D	STU STAUROSPORINE × 2 32H 2-bromo-3-(4-bromophenyl)-4-hydroxy-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile × 2 CL CHLORIDE ION × 10 AMP ADENOSINE MONOPHOSPHATE × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；750 mM Ammonium Sulfate, 500 mM Lithium Sulfate, 100 mM tri-Sodium Citrate, 1% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.55 Å R-free 0.269
4YEF beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin Deposited 2015-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 76–156（81 aa） Fragment：UNP residues 76-156	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；281.15 K；0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5	Resolution 1.72 Å R-free 0.213
4YEF beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin Deposited 2015-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 76–156（81 aa） Fragment：UNP residues 76-156	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；281.15 K；0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5	Resolution 1.72 Å R-free 0.213
4YEF beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin Deposited 2015-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 76–156（81 aa） Fragment：UNP residues 76-156	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；281.15 K；0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5	Resolution 1.72 Å R-free 0.213
4YEF beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin Deposited 2015-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 76–156（81 aa） Fragment：UNP residues 76-156	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；281.15 K；0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5	Resolution 1.72 Å R-free 0.213
4YEF beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin Deposited 2015-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain E 76–156（81 aa） Fragment：UNP residues 76-156	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；281.15 K；0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5	Resolution 1.72 Å R-free 0.213
4YEF beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin Deposited 2015-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain F 76–156（81 aa） Fragment：UNP residues 76-156	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；281.15 K；0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5	Resolution 1.72 Å R-free 0.213
4YEF beta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin Deposited 2015-02-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 7 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain G 76–156（81 aa） Fragment：UNP residues 76-156	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；281.15 K；0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5	Resolution 1.72 Å R-free 0.213
5KQ5 AMPK bound to allosteric activator Deposited 2016-07-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa） Fragment：residues 68-270	Mutation：S108D	STU STAUROSPORINE × 1 6VT 6-chloranyl-5-[4-(1-oxidanylcyclobutyl)phenyl]-1~{H}-indole-3-carboxylic acid × 1 CL CHLORIDE ION × 4 AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；~750 mM Ammonium Acetate, 500 mM Lithium Sulfate, 100 mM trisodium citrate, 1% ethylene glycol	Resolution 3.41 Å R-free 0.259
5T5T AMPK bound to allosteric activator Deposited 2016-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa）	Mutation：S108D, Q109H	STU STAUROSPORINE × 1 CL CHLORIDE ION × 3 SO4 SULFATE ION × 2 75O 6-chloro-5-[6-(dimethylamino)-2-methoxypyridin-3-yl]-1H-indole-3-carboxylic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；100 mM trisodium citrate, 500 mM ammonium sulfate, 900 mM lithium sulfate, and 4% glycerol	Resolution 3.46 Å R-free 0.231
5T5T AMPK bound to allosteric activator Deposited 2016-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa）	Mutation：S108D, Q109H	STU STAUROSPORINE × 2 CL CHLORIDE ION × 6 SO4 SULFATE ION × 4 75O 6-chloro-5-[6-(dimethylamino)-2-methoxypyridin-3-yl]-1H-indole-3-carboxylic acid × 2 AMP ADENOSINE MONOPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；100 mM trisodium citrate, 500 mM ammonium sulfate, 900 mM lithium sulfate, and 4% glycerol	Resolution 3.46 Å R-free 0.231
5UFU Structure of AMPK bound to activator Deposited 2017-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa）	Not recorded	STU STAUROSPORINE × 1 85V 1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol × 1 CL CHLORIDE ION × 3 SO4 SULFATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 mM ammonium sulfate 500 mM lithium sulfate 100 mM trisodium citrate 1% ethylene glycol	Resolution 3.45 Å R-free 0.238
5UFU Structure of AMPK bound to activator Deposited 2017-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa）	Not recorded	STU STAUROSPORINE × 2 85V 1,4:3,6-dianhydro-2-O-(6-chloro-5-{4-[1-(hydroxymethyl)cyclopropyl]phenyl}-1H-benzimidazol-2-yl)-D-mannitol × 2 CL CHLORIDE ION × 6 SO4 SULFATE ION × 4 AMP ADENOSINE MONOPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 mM ammonium sulfate 500 mM lithium sulfate 100 mM trisodium citrate 1% ethylene glycol	Resolution 3.45 Å R-free 0.238
6E4T Structure of AMPK bound to activator Deposited 2018-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HTV 1-O-{6-chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1H-indole-3-carbonyl}-beta-D-glucopyranuronic acid × 1 STU STAUROSPORINE × 1 CL CHLORIDE ION × 5 AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL	Resolution 3.40 Å R-free 0.245
6E4T Structure of AMPK bound to activator Deposited 2018-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HTV 1-O-{6-chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1H-indole-3-carbonyl}-beta-D-glucopyranuronic acid × 2 STU STAUROSPORINE × 2 CL CHLORIDE ION × 10 AMP ADENOSINE MONOPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL	Resolution 3.40 Å R-free 0.245
6E4U Structure of AMPK bound to activator Deposited 2018-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 HU7 1-O-{6-chloro-5-[6-(dimethylamino)-2-methoxypyridin-3-yl]-1H-indole-3-carbonyl}-beta-D-glucopyranuronic acid × 1 CL CHLORIDE ION × 4 AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL	Resolution 3.27 Å R-free 0.231
6E4U Structure of AMPK bound to activator Deposited 2018-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 2 HU7 1-O-{6-chloro-5-[6-(dimethylamino)-2-methoxypyridin-3-yl]-1H-indole-3-carbonyl}-beta-D-glucopyranuronic acid × 2 CL CHLORIDE ION × 8 AMP ADENOSINE MONOPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL	Resolution 3.27 Å R-free 0.231
6E4W Structure of AMPK bound to activator Deposited 2018-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 68–270（203 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 HUG 1-O-(4,6-difluoro-5-{4-[(2S)-oxan-2-yl]phenyl}-1H-indole-3-carbonyl)-beta-D-glucopyranuronic acid × 1 CL CHLORIDE ION × 3 AMP ADENOSINE MONOPHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL	Resolution 3.35 Å R-free 0.244
6E4W Structure of AMPK bound to activator Deposited 2018-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 68–270（203 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 2 HUG 1-O-(4,6-difluoro-5-{4-[(2S)-oxan-2-yl]phenyl}-1H-indole-3-carbonyl)-beta-D-glucopyranuronic acid × 2 CL CHLORIDE ION × 6 AMP ADENOSINE MONOPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；750 MM AMMONIUM SULFATE, 500 MM LITHIUM SULFATE, 100 MM TRISODIUM CITRATE, 1% ETHYLENE GLYCOL	Resolution 3.35 Å R-free 0.244

14 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AAKB_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–96； UniProt 67–162 Author chain B； PDBConstruct 1–96； UniProt 67–162 Author chain C； PDBConstruct 1–96； UniProt 67–162

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	1z0n
Deposition date deposition_date	2005-03-02
Structure title title	the glycogen-binding domain of the AMP-activated protein kinase
Keywords keywords	beta sandwich, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	23.77 Å
Radius of gyration Rg (electron density) rg_electron	23.21 Å
Forward intensity I(0) i0	17535900.00
Molecular weight molecular_weight	31645.0 kDa
Excluded volume excluded_volume	39461 Å³
Envelope volume envelope_volume	48252 Å³
Hydration-shell volume shell_volume	18819 Å³
Envelope diameter envelope_diameter	83.1 Å
Shell Rg shell_rg	27.85 Å
Envelope Rg envelope_rg	23.15 Å
Shape Rg shape_rg	23.15 Å
Total Rg total_rg	23.99 Å
Total atoms total_atoms	2223
Residues n_residues	244
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	81.9 Å
Rg (real space) rg_real	23.89 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	1.7540e+07
I(0) uncertainty (real space) i0_real_error	2.4270e+05
Rg (reciprocal space) rg_reciprocal	23.86 Å
I(0) (reciprocal space) i0_reciprocal	17540000.0000
Solution quality estimate total_estimate	0.8681
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.433
Kurtosis Kurtosis kurtosis	-0.322
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3366000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.798; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;5'-AMP-activated protein kinase, beta-1 subunit ;
Molecular weight formula_weight	10973.0 kDa
Mutation mutation	L105M
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2530

EVNEKAPAQARPTVFRWTGGGKEVYLSGSFNNWSKLPMTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVF

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	Cycloheptakis-(1-4)-(alpha-D-glucopyranose)
Molecular weight formula_weight	1153.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	307

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1z0na1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.21 — AMPK-beta glycogen binding domain-like

Domain ID domain_id	d1z0nb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.21 — AMPK-beta glycogen binding domain-like

Domain ID domain_id	d1z0nc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.21 — AMPK-beta glycogen binding domain-like

CATH v4.4 (3 domains)

Domain ID domain_id	1z0nA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1z0nB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1z0nC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (2)

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Unit-cell length a length_a	43.750 Å
Unit-cell length b length_b	45.250 Å
Unit-cell length c length_c	50.600 Å
Unit-cell angle α angle_alpha	71.90 °
Unit-cell angle β angle_beta	69.70 °
Unit-cell angle γ angle_gamma	65.40 °
Molecules per unit cell Z z_pdb	3

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.490 Å
Low-resolution limit resolution_low	23.270 Å
R factor r_factor	0.1840
R_work r_work	0.1839
R_free r_free	0.2126

fit	/app/data/saxs_computation/z0/1z0n/1z0n.fit
pddf	/app/data/pr_computation/z0/1z0n/1z0n.pr.out
profile	/app/data/saxs_computation/z0/1z0n/1z0n.dat