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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q9Y478 New Search
12PDB entries
20Biological assembly
20chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
4CFE Structure of full length human AMPK in complex with a small molecule activator, a benzimidazole derivative (991) Deposited 2013-11-14 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 1–270（270 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 1–270（270 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 1–270（270 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 Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 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 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 Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 1–270（270 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 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 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；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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 1–270（270 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；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 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 1–270（270 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
6C9F AMP-activated protein kinase bound to pharmacological activator R734 Deposited 2018-01-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 68–270（203 aa）
Not recorded R34 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide × 1 STU STAUROSPORINE × 1 AMP ADENOSINE MONOPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M tri-sodium acetate pH 5.6, 0.2 M ammonium acetate, 15% w/v PEG 4000
Resolution 2.92 Å R-free 0.245
6C9G AMP-activated protein kinase bound to pharmacological activator R739 Deposited 2018-01-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 68–270（203 aa）
Not recorded R93 5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide × 1 STU STAUROSPORINE × 1 AMP ADENOSINE MONOPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M tri-sodium acetate pH 5.6, 0.2 M ammonium acetate, 15% w/v PEG 4000
Resolution 2.70 Å R-free 0.240
6C9H non-phosphorylated AMP-activated protein kinase bound to pharmacological activator R734 Deposited 2018-01-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 68–270（203 aa）
Not recorded R34 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide × 1 STU STAUROSPORINE × 1 AMP ADENOSINE MONOPHOSPHATE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M magnesium formate
Resolution 2.65 Å R-free 0.242
6C9J AMP-activated protein kinase bound to pharmacological activator R734 Deposited 2018-01-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 68–270（203 aa）
Not recorded R34 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide × 1 STU STAUROSPORINE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M tri-ammonium citrate pH7, 12% w/v PEG 3350
Resolution 3.05 Å R-free 0.225
7MYJ Structure of full length human AMPK (a2b1g1) in complex with a small molecule activator MSG011 Deposited 2021-05-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 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 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 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 1–270（270 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 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 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–270（270 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) STU STAUROSPORINE × 1 QTN (3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$l^{4}-sulfanyl]amino]phenyl]phenyl]-3~{H}-imidazo[4,5-b]pyridin-2-yl]oxy]-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-3-ol × 1 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；AMPK a2b1g1 (5 mg/ml: 38 uM) was combined with AMP (4-fold excess), staurosporine (1.2-fold excess) and activator 455 (3-fold excess): and crystallised at 20 C by mixing 2 ul of the protein solution with 1 ul of 8 % PEG3350, 0.3 M guanidine hydrochloride, 0.1 M PIPES buffer pH 7.2.
Resolution 2.50 Å R-free 0.215
8BIK Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455 Deposited 2022-11-02 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain E 1–270（270 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) STU STAUROSPORINE × 1 QTN (3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.