8bik

Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	;5'-AMP-activated protein kinase subunit beta-1 ; × 1 （Q9Y478） ;5'-AMP-activated protein kinase subunit gamma-1 ; × 1 （P54619） STAUROSPORINE × 1 ;(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$l^{4}-sulfanyl]amino]phenyl]phenyl]-3~{H}-imidazo[4,5-b]pyridin-2-yl]oxy]-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-3-ol ; × 1 ADENOSINE MONOPHOSPHATE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	;5'-AMP-activated protein kinase subunit beta-1 ; × 1 （Q9Y478） ;5'-AMP-activated protein kinase subunit gamma-1 ; × 1 （P54619） STAUROSPORINE × 1 ;(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$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 ADENOSINE MONOPHOSPHATE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AAPK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–559； UniProt 1–552 Author chain D； PDBConstruct 8–559； UniProt 1–552

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

Homo sapiens

UniProt Q9Y478

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	;5'-AMP-activated protein kinase catalytic subunit alpha-2 ; × 1 （P54646） ;5'-AMP-activated protein kinase subunit gamma-1 ; × 1 （P54619） STAUROSPORINE × 1 ;(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$l^{4}-sulfanyl]amino]phenyl]phenyl]-3~{H}-imidazo[4,5-b]pyridin-2-yl]oxy]-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-3-ol ; × 1 ADENOSINE MONOPHOSPHATE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	;5'-AMP-activated protein kinase catalytic subunit alpha-2 ; × 1 （P54646） ;5'-AMP-activated protein kinase subunit gamma-1 ; × 1 （P54619） STAUROSPORINE × 1 ;(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$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 ADENOSINE MONOPHOSPHATE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AAKB1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–270； UniProt 1–270 Author chain E； PDBConstruct 1–270； UniProt 1–270

;5'-AMP-activated protein kinase subunit gamma-1 ;

Homo sapiens

UniProt P54619

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	;5'-AMP-activated protein kinase catalytic subunit alpha-2 ; × 1 （P54646） ;5'-AMP-activated protein kinase subunit beta-1 ; × 1 （Q9Y478） STAUROSPORINE × 1 ;(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$l^{4}-sulfanyl]amino]phenyl]phenyl]-3~{H}-imidazo[4,5-b]pyridin-2-yl]oxy]-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]furan-3-ol ; × 1 ADENOSINE MONOPHOSPHATE × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	;5'-AMP-activated protein kinase catalytic subunit alpha-2 ; × 1 （P54646） ;5'-AMP-activated protein kinase subunit beta-1 ; × 1 （Q9Y478） STAUROSPORINE × 1 ;(3~{R},3~{a}~{R},6~{R},6~{a}~{R})-6-[[6-chloranyl-5-[4-[4-[[dimethyl(oxidanyl)-$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 ADENOSINE MONOPHOSPHATE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AAKG1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–331； UniProt 1–331 Author chain F； PDBConstruct 1–331； UniProt 1–331

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	8bik
Deposition date deposition_date	2022-11-02
Structure title title	Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455
Keywords keywords	AMPK activator, allosteric activator, ADaM site, structure-based drug design, selectivity, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8bik__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8bik__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8bik__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.30 Å
Rg (electron density)	33.86 Å
Total Rg	34.20 Å
Atom count	7573
Residues	931
Excluded volume	135870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8bik__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8bik__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	;5'-AMP-activated protein kinase catalytic subunit alpha-2 ;
Molecular weight formula_weight	63368.7 kDa
EC 编号 ec_number	2.7.11.1,2.7.11.27,2.7.11.31
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	15482

MHHHHHHMAEKQKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFKQDLPSYLFPEDPSYDANVIDDEAVKEVCEKFECTESEVMNSLYSGDPQDQLAVAYHLIIDNRRIMNQASEFYLASSPPSGSFMDDSAMHIPPGLKPHPERMPPLIADSPKARCPLDALNTTKPKSLAVKKAKWHLGIRSQSKPYDIMAEVYRAMKQLDFEWKVVNAYHLRVRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDDEVVEQRSGSSTPQRSCSAAGLHRPRSSFDSTTAESHSLSGSLTGSLTGSTLSSVSPRLGSHTMDFFEMCASLITTLAR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;5'-AMP-activated protein kinase subunit beta-1 ;
Molecular weight formula_weight	30504.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGNTSSERAALERHGGHKTPRRDSSGGTKDGDRPKILMDSPEDADLFHSEEIKAPEKEEFLAWQHDLEVNDKAPAQARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRSHNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKCSDVSELSSSPPGPYHQEPYVCKPEERFRAPPILPPHLLQVILNKDTGISCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	;5'-AMP-activated protein kinase subunit gamma-1 ;
Molecular weight formula_weight	37626.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

METVISSDSSPAVENEHPQETPESNNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEVHRLVVVDENDVVKGIVSLSDILQALVLTGGEKKP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	STAUROSPORINE
Molecular weight formula_weight	466.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	543.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	482

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Unit-cell length a length_a	75.313 Å
Unit-cell length b length_b	127.975 Å
Unit-cell length c length_c	139.215 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	69.520 Å
R factor r_factor	0.1830
R_work r_work	0.1810
R_free r_free	0.2150

Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455

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

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

State in the Current Structure

Other States of the Same Protein in the Database

;5'-AMP-activated protein kinase subunit gamma-1 ;

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8bik__assembly_1__model_1

8bik__assembly_1__model_1 | I(q)

8bik__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;5'-AMP-activated protein kinase subunit gamma-1 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8bik__assembly_1__model_1

8bik__assembly_1__model_1 | I(q)

8bik__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)