6b1u

Structure of full-length human AMPK (a2b1g1) in complex with a small molecule activator SC4

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 ;5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid ; × 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 ;5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid ; × 1 IMIDAZOLE × 1 ADENOSINE MONOPHOSPHATE × 2 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 15–565； UniProt 2–552 Author chain C； PDBConstruct 15–565； UniProt 2–552

;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 ;5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid ; × 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 ;5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid ; × 1 IMIDAZOLE × 1 ADENOSINE MONOPHOSPHATE × 2 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 D； 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 ;5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid ; × 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 ;5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid ; × 1 IMIDAZOLE × 1 ADENOSINE MONOPHOSPHATE × 2 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 E； PDBConstruct 7–336； UniProt 2–331 Author chain F； PDBConstruct 7–336； UniProt 2–331

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	6b1u
Deposition date deposition_date	2017-09-19
Structure title title	Structure of full-length human AMPK (a2b1g1) in complex with a small molecule activator SC4
Keywords keywords	Phosphorylated, Active, Heterotrimer, Kinase., TRANSFERASE; TRANSFERASE
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.

6b1u__assembly_1__model_1

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

Download this curve (.dat)

6b1u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6b1u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.48 Å
Rg (electron density)	34.16 Å
Total Rg	34.42 Å
Atom count	7304
Residues	923
Excluded volume	130840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6b1u__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6b1u__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 (8)

Entity 1 Entity 1 polymer

Description description	;5'-AMP-activated protein kinase catalytic subunit alpha-2 ;
Molecular weight formula_weight	63918.1 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,C
Atom count atom_count	14977

MGSSHHHHHHSQDPAEKQKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFKQGLPSYLFPEDPSYDANVIDDEAVKEVCEKFECTESEVMNSLYSGDPQDQLAVAYHLIIDNRRIMNQASEFYLASSPPSGSFMDDSAMHIPPGLKPHPERMPPLIADSPKARCPLDALNTTKPKSLAVKKAKWHLGIRSQSKPYDIMAEVYRAMKQLDFEWKVVNAYHLRVRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDDEVVEQRSGSSTPQRSCSAAGLHRPRSSFDSTTAESHSLSGSLTGSLTGSTLSSVSPRLGSHTMDFFEMCASLITTLAR

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

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,D

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

Entity 3 Entity 3 polymer

Description description	;5'-AMP-activated protein kinase subunit gamma-1 ;
Molecular weight formula_weight	38225.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MADLNWETVISSDSSPAVENEHPQETPESNNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEVHRLVVVDENDVVKGIVSLSDILQALVLTGGEKKP

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

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	;5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid ;
Molecular weight formula_weight	471.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6b1ue1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d6b1ue2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d6b1uf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

Domain ID domain_id	d6b1uf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.37 — CBS-domain pair
Superfamily Superfamily superfamily	d.37.1 — CBS-domain pair
Family Family family	d.37.1.1 — CBS-domain pair

CATH v4.4 (2 domains)

Domain ID domain_id	6b1uA01
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

Domain ID domain_id	6b1uC01
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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Unit-cell length a length_a	75.827 Å
Unit-cell length b length_b	133.897 Å
Unit-cell length c length_c	141.725 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.74 °
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	2.770 Å
Low-resolution limit resolution_low	48.640 Å
R factor r_factor	0.1960
R_work r_work	0.1940
R_free r_free	0.2260

Structure of full-length human AMPK (a2b1g1) in complex with a small molecule activator SC4

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

6b1u__assembly_1__model_1

6b1u__assembly_1__model_1 | I(q)

6b1u__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of full-length human AMPK (a2b1g1) in complex with a small molecule activator SC4

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

6b1u__assembly_1__model_1

6b1u__assembly_1__model_1 | I(q)

6b1u__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 (8)

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 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)