SAXSdb — 2yza

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

;5'-AMP-activated protein kinase catalytic subunit alpha-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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 6–279	Fragment：kinase domain Mutation：T172D	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；0.1M Tris-HCl pH8.9, 16% PEG4000, 15% isopropanol, 0.1M Ammonium sulfate, Protein solution: 5mM AMPPNP, 5mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.02 Å R-free 0.308

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 2YZA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2H6D Protein Kinase Domain of the Human 5'-AMP-activated protein kinase catalytic subunit alpha-2 (AMPK alpha-2 chain) Deposited 2006-05-31	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–279（274 aa） Fragment：KINASE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；18.6% PEG 4000, 0.1M AmSO4, 0.1M Tris-HCl pH 8.5, 15%v/v isopropanol,5mM ATP/MgCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.85 Å R-free 0.227
2LTU Solution Structure of autoinhibitory domain of human AMP-activated protein kinase catalytic subunit Deposited 2012-06-01	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 282–339（58 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.2 mM [U-100% 13C; U-100% 15N] AID protein, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 90 % H2O, 1 mM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3AQV Human AMP-activated protein kinase alpha 2 subunit kinase domain (T172D) complexed with compound C Deposited 2010-11-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–279（274 aa） Fragment：kinase domain	Mutation：T172D	TAK 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；293 K；0.1M Bis-Tris (pH 6.5), 1.5M ammonium sulfate, 0.1M NaCl, 0.5mM Compound C, 5mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.08 Å R-free 0.281
4CFE Structure of full length human AMPK in complex with a small molecule activator, a benzimidazole derivative (991) Deposited 2013-11-14	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 C 1–552（552 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 992 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 13% PEG3350, 0.1M MGCL2, 1% GLUCOSE, 0.15% CAPB IN 0.1M IMIDAZOLE AT PH 6.2.	Resolution 3.02 Å R-free 0.253
4CFE Structure of full length human AMPK in complex with a small molecule activator, a benzimidazole derivative (991) Deposited 2013-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–552（552 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 992 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 13% PEG3350, 0.1M MGCL2, 1% GLUCOSE, 0.15% CAPB IN 0.1M IMIDAZOLE AT PH 6.2.	Resolution 3.02 Å R-free 0.253
4CFF Structure of full length human AMPK in complex with a small molecule activator, a thienopyridone derivative (A-769662) Deposited 2013-11-14	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 C 1–552（552 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 C1V 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 13% PEG3350, 0.1M MGCL2, 1% GLUCOSE, 0.15% CAPB IN 0.1M IMIDAZOLE AT PH 6.2.	Resolution 3.92 Å R-free 0.264
4CFF Structure of full length human AMPK in complex with a small molecule activator, a thienopyridone derivative (A-769662) Deposited 2013-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–552（552 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 C1V 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 13% PEG3350, 0.1M MGCL2, 1% GLUCOSE, 0.15% CAPB IN 0.1M IMIDAZOLE AT PH 6.2.	Resolution 3.92 Å R-free 0.264
4ZHX Novel binding site for allosteric activation of AMPK Deposited 2015-04-27	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 A 2–552（551 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	4O7 (5S,6R,7R,9R,13cR,14R,16aS)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16a-octahydro-5H,13cH-5,9-epoxy-4b,9a,1 5-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-ol × 1 C1V 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile × 1 C2Z 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；8 % PEG 3350, 0.1 M MgCl2, 1.0 % glucose, 0.001 % cocamidopropyl betaine, 0.1 M imidazole	Resolution 2.99 Å R-free 0.243
4ZHX Novel binding site for allosteric activation of AMPK Deposited 2015-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–552（551 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	4O7 (5S,6R,7R,9R,13cR,14R,16aS)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16a-octahydro-5H,13cH-5,9-epoxy-4b,9a,1 5-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-ol × 1 C1V 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；8 % PEG 3350, 0.1 M MgCl2, 1.0 % glucose, 0.001 % cocamidopropyl betaine, 0.1 M imidazole	Resolution 2.99 Å R-free 0.243
5EZV X-ray crystal structure of AMP-activated protein kinase alpha-2/alpha-1 RIM chimaera (alpha-2(1-347)/alpha-1(349-401)/alpha-2(397-end) beta-1 gamma-1) co-crystallized with C2 (5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid) Deposited 2015-11-26	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 A 2–347（346 aa） Chain A 397–552（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 C1V 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile × 1 C2Z 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；8 % PEG 3350, 0.1 M MgCl2, 1.0 % glucose, 0.001 % cocamidopropyl betaine, 0.1 M imidazole	Resolution 2.99 Å R-free 0.245
5EZV X-ray crystal structure of AMP-activated protein kinase alpha-2/alpha-1 RIM chimaera (alpha-2(1-347)/alpha-1(349-401)/alpha-2(397-end) beta-1 gamma-1) co-crystallized with C2 (5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid) Deposited 2015-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–347（346 aa） Chain C 397–552（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 C1V 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile × 1 C2Z 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；8 % PEG 3350, 0.1 M MgCl2, 1.0 % glucose, 0.001 % cocamidopropyl betaine, 0.1 M imidazole	Resolution 2.99 Å R-free 0.245
5ISO STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991) Deposited 2016-03-15	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 A 1–552（552 aa）	Not recorded	STU STAUROSPORINE × 1 992 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；12% PEG3350, 300 mM Guanidine in 100mM PIPES buffer at pH 7.2.	Resolution 2.63 Å R-free 0.230
5ISO STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991) Deposited 2016-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–552（552 aa）	Not recorded	STU STAUROSPORINE × 1 992 5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；12% PEG3350, 300 mM Guanidine in 100mM PIPES buffer at pH 7.2.	Resolution 2.63 Å R-free 0.230
6B1U Structure of full-length human AMPK (a2b1g1) in complex with a small molecule activator SC4 Deposited 2017-09-19	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 A 2–552（551 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 CG7 5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；8% PEG 3350, 0.1 M MgCl2, 1.0% glucose, 0.001% cocamidopropyl betaine and 0.1 M imidazole.	Resolution 2.77 Å R-free 0.226
6B1U Structure of full-length human AMPK (a2b1g1) in complex with a small molecule activator SC4 Deposited 2017-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–552（551 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 CG7 5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid × 1 IMD IMIDAZOLE × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；8% PEG 3350, 0.1 M MgCl2, 1.0% glucose, 0.001% cocamidopropyl betaine and 0.1 M imidazole.	Resolution 2.77 Å R-free 0.226
6B2E Structure of full length human AMPK (a2b2g1) in complex with a small molecule activator SC4. Deposited 2017-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–552（551 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 CG7 5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；6-8% PEG 3350, 0.1 M MgCl2, 0.001% cocamidopropyl betaine and 0.1 M imidazole	Resolution 3.80 Å R-free 0.277
6BX6 AMP-Activated protein kinase (AMPK) inhibition by SBI-0206965: alpha 2 kinase domain bound to SBI-0206965 Deposited 2017-12-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–279（274 aa）	Mutation：T172D	EDJ 2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；9-14 % ethanol, 5 mM magnesium chloride, 3-7 mM manganese chloride, 10 mM TCEP and 0.1 M Tris, pH 9.5.	Resolution 2.90 Å R-free 0.280
7MYJ Structure of full length human AMPK (a2b1g1) in complex with a small molecule activator MSG011 Deposited 2021-05-21	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 A 2–552（551 aa）	Mutation：D271G Non-standard monomer：Yes (specific site not provided by mmCIF)	4O7 (5S,6R,7R,9R,13cR,14R,16aS)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16a-octahydro-5H,13cH-5,9-epoxy-4b,9a,1 5-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-ol × 1 ZQV 5-({5-[(4'R)-4'-acetamido-2',3',4',5'-tetrahydro[1,1'-biphenyl]-4-yl]-6-chloro-1H-imidazo[4,5-b]pyridin-2-yl}oxy)-2-methylbenzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277.15 K；8-10% PEG3350, 1% glucose, 0.1 M magnesium chloride, 0.1 M imidazole, 0.0005-0.003% CAPB	Resolution 2.95 Å R-free 0.243
7MYJ Structure of full length human AMPK (a2b1g1) in complex with a small molecule activator MSG011 Deposited 2021-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–552（551 aa）	Mutation：D271G Non-standard monomer：Yes (specific site not provided by mmCIF)	4O7 (5S,6R,7R,9R,13cR,14R,16aS)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16a-octahydro-5H,13cH-5,9-epoxy-4b,9a,1 5-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-ol × 1 ZQV 5-({5-[(4'R)-4'-acetamido-2',3',4',5'-tetrahydro[1,1'-biphenyl]-4-yl]-6-chloro-1H-imidazo[4,5-b]pyridin-2-yl}oxy)-2-methylbenzoic acid × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277.15 K；8-10% PEG3350, 1% glucose, 0.1 M magnesium chloride, 0.1 M imidazole, 0.0005-0.003% CAPB	Resolution 2.95 Å R-free 0.243
8BIK Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455 Deposited 2022-11-02	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 A 1–552（552 aa）	Not recorded	STU STAUROSPORINE × 1 QTN (3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$l^{4}-sulfanyl]amino]phenyl]phenyl]-3~{H}-imidazo[4,5-b]pyridin-2-yl]oxy]-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-3-ol × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；AMPK a2b1g1 (5 mg/ml: 38 uM) was combined with AMP (4-fold excess), staurosporine (1.2-fold excess) and activator 455 (3-fold excess): and crystallised at 20 C by mixing 2 ul of the protein solution with 1 ul of 8 % PEG3350, 0.3 M guanidine hydrochloride, 0.1 M PIPES buffer pH 7.2.	Resolution 2.50 Å R-free 0.215
8BIK Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455 Deposited 2022-11-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–552（552 aa）	Not recorded	STU STAUROSPORINE × 1 QTN (3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$l^{4}-sulfanyl]amino]phenyl]phenyl]-3~{H}-imidazo[4,5-b]pyridin-2-yl]oxy]-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-3-ol × 1 AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；AMPK a2b1g1 (5 mg/ml: 38 uM) was combined with AMP (4-fold excess), staurosporine (1.2-fold excess) and activator 455 (3-fold excess): and crystallised at 20 C by mixing 2 ul of the protein solution with 1 ul of 8 % PEG3350, 0.3 M guanidine hydrochloride, 0.1 M PIPES buffer pH 7.2.	Resolution 2.50 Å R-free 0.215
9IC2 Structure of AMPK-alpha2-kinase domain bound to BAY-3827 Deposited 2025-02-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–280（275 aa）	Not recorded	A1I1Y ~{N}-[5-(3,5-dicyano-1,2,6-trimethyl-4~{H}-pyridin-4-yl)-6-fluoranyl-7-methyl-1~{H}-indazol-3-yl]-2-ethyl-benzamide × 1 MG MAGNESIUM ION × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.1M Ammonium sulfate, 0.3 Sodium formate, 0.1M Sodium cacodylate pH 6.5, 3% Gamma-PGA, 3% PEG 20000	Resolution 2.50 Å R-free 0.235

14 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AAPK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–276； UniProt 6–279

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2yza
Deposition date deposition_date	2007-05-04
Structure title title	Crystal structure of kinase domain of Human 5'-AMP-activated protein kinase alpha-2 subunit mutant (T172D)
Keywords keywords	;Signaling protein, Serine/threonine protein kinase, Phosphorylation, ATP-binding, Nucleotide-binding, Cholesterol biosynthesis, Fatty acid biosynthesis, Lipid synthesis, glucose metabolism, Magnesium, Metal-binding, Serine/threonine-protein kinase, Steroid biosynthesis, Transferase, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI ;; 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	20.51 Å
Radius of gyration Rg (electron density) rg_electron	19.49 Å
Forward intensity I(0) i0	14054900.00
Molecular weight molecular_weight	29285.0 kDa
Excluded volume excluded_volume	37210 Å³
Envelope volume envelope_volume	45129 Å³
Hydration-shell volume shell_volume	19679 Å³
Envelope diameter envelope_diameter	66.6 Å
Shell Rg shell_rg	25.39 Å
Envelope Rg envelope_rg	19.54 Å
Shape Rg shape_rg	19.48 Å
Total Rg total_rg	20.42 Å
Total atoms total_atoms	2063
Residues n_residues	258
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	64.6 Å
Rg (real space) rg_real	20.43 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.4050e+07
I(0) uncertainty (real space) i0_real_error	1.7150e+05
Rg (reciprocal space) rg_reciprocal	20.45 Å
I(0) (reciprocal space) i0_reciprocal	14050000.0000
Solution quality estimate total_estimate	0.9010
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.360
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2458000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.992

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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2yzaa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2yzaA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	2yzaA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	39.187 Å
Unit-cell length b length_b	67.336 Å
Unit-cell length c length_c	50.651 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.020 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2350
R_work r_work	0.2270
R_free r_free	0.3080

Description description	;5'-AMP-activated protein kinase catalytic subunit alpha-2 ;
Molecular weight formula_weight	31571.7 kDa
EC 编号 ec_number	2.7.11.1
Mutation mutation	T172D
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2073

Crystal structure of kinase domain of Human 5'-AMP-activated protein kinase alpha-2 subunit mutant (T172D)

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

;5'-AMP-activated protein kinase catalytic subunit alpha-2 ;

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Cell-free protein synthesis

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	10

fit	/app/data/saxs_computation/yz/2yza/2yza.fit
pddf	/app/data/pr_computation/yz/2yza/2yza.pr.out
profile	/app/data/saxs_computation/yz/2yza/2yza.dat