SAXSdb — 4red

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

;5'-AMP-activated protein kinase catalytic subunit alpha-1 ;

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 22–362 Chain B； UniProt 22–362	Fragment：human AMPK KD-AID, UNP residues 22-362 Mutation：K43A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.5 M HNa2PO4/0.5 M HK2PO4, 0.1 M Tris hydrochloride, pH 8.5, 0.1 M H(NH4)2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.95 Å R-free 0.277
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 22–362 Chain B； UniProt 22–362	Fragment：human AMPK KD-AID, UNP residues 22-362 Mutation：K43A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.5 M HNa2PO4/0.5 M HK2PO4, 0.1 M Tris hydrochloride, pH 8.5, 0.1 M H(NH4)2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.95 Å R-free 0.277
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 22–362 Chain B； UniProt 22–362	Fragment：human AMPK KD-AID, UNP residues 22-362 Mutation：K43A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.5 M HNa2PO4/0.5 M HK2PO4, 0.1 M Tris hydrochloride, pH 8.5, 0.1 M H(NH4)2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.95 Å R-free 0.277

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 4RED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4RER Crystal structure of the phosphorylated human alpha1 beta2 gamma1 holo-AMPK complex bound to AMP and cyclodextrin Deposited 2014-09-23	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 20–559（540 aa） Fragment：Human AMPK alpha1 subunit [G11-Q550]	Mutation：E471G, E474A, K476A Non-standard monomer：Yes (specific site not provided by mmCIF)	STU STAUROSPORINE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；12% PEG 4000,0.1 M HEPES, pH7.8, 10% 2-propanol (v/v) and 0.19 mM 7-cyclohexyl-1-heptyl-D-maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 4.05 Å R-free 0.260
4REW Crystal structure of the non-phosphorylated human alpha1 beta2 gamma1 holo-AMPK complex Deposited 2014-09-24	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 20–559（540 aa） Fragment：Human AMPK alpha1 subunit [G11-Q550]	Mutation：E471G, E474A, K476A	STU STAUROSPORINE × 1 AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；293 K；0.1 M N-acetamido-iminodiacetic acid, pH 6.8, 9% 2-methyl-2,4-pentanediol, and 11.5 mM C-HEGA, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 4.58 Å R-free 0.259
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 359–401（43 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	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 359–401（43 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
6C9F AMP-activated protein kinase bound to pharmacological activator R734 Deposited 2018-01-26	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 22–480（459 aa） Chain A 535–559（25 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	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	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 22–480（459 aa） Chain A 535–559（25 aa）	Mutation：S108D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S108D Non-standard monomer：Yes (specific site not provided by mmCIF)	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	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 22–480（459 aa） Chain A 535–559（25 aa）	Mutation：S108D Mutation：S108D	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	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 22–480（459 aa） Chain A 535–559（25 aa）	Mutation：S108D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S108D Non-standard monomer：Yes (specific site not provided by mmCIF)	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
7JHG Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Dorsomorphin (Compound C) and Fab-nanobody Deposited 2020-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 22–480（459 aa） Fragment：UNP residues 22-480,535-559 Chain A 535–559（25 aa） Fragment：UNP residues 22-480,535-559	Not recorded	TAK 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
7JHH Cryo-EM structure of ATP-bound fully inactive AMPK in complex with Fab and nanobody Deposited 2020-07-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 22–480（459 aa） Fragment：UNP residues 22-480,535-559 Chain A 535–559（25 aa） Fragment：UNP residues 22-480,535-559	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.92 Å
7JIJ ATP-bound AMP-activated protein kinase Deposited 2020-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–559（538 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M tri-lithium citrate,10% w/v PEG3350, pH7.5,0.01 M barium chloride	Resolution 5.50 Å R-free 0.323

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AAPK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–351； UniProt 22–362 Author chain B； PDBConstruct 11–351； UniProt 22–362

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	4red
Deposition date deposition_date	2014-09-22
Structure title title	Crystal structure of human AMPK alpha1 KD-AID with K43A mutation
Keywords keywords	;Kinase Domain Fold, phosphorylate numerous cellular targets, upregulate ATP-generating pathways upon activation, AMPK beta and gamma subunits, TRANSFERASE ;; 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	29.02 Å
Radius of gyration Rg (electron density) rg_electron	28.23 Å
Forward intensity I(0) i0	89213100.00
Molecular weight molecular_weight	75242.0 kDa
Excluded volume excluded_volume	94759 Å³
Envelope volume envelope_volume	122700 Å³
Hydration-shell volume shell_volume	35773 Å³
Envelope diameter envelope_diameter	97.8 Å
Shell Rg shell_rg	35.92 Å
Envelope Rg envelope_rg	27.77 Å
Shape Rg shape_rg	28.21 Å
Total Rg total_rg	29.09 Å
Total atoms total_atoms	5293
Residues n_residues	659
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	92.2 Å
Rg (real space) rg_real	28.90 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	8.9210e+07
I(0) uncertainty (real space) i0_real_error	1.4350e+06
Rg (reciprocal space) rg_reciprocal	28.95 Å
I(0) (reciprocal space) i0_reciprocal	89220000.0000
Solution quality estimate total_estimate	0.9030
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.6 Å
Skewness Skewness skewness	0.160
Kurtosis Kurtosis kurtosis	-0.501
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27970000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	;5'-AMP-activated protein kinase catalytic subunit alpha-1 ;
Molecular weight formula_weight	40200.2 kDa
EC 编号 ec_number	2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26
Mutation mutation	K43A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5323

MGHHHHHHGSVKIGHYILGDTLGVGTFGKVKVGKHELTGHAVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRASIKDIREHEWFKQDLPKYLFPEDPSYSTTMIDDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAKDFYLATSPPDSFL

来源 Source

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	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4redA01
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	4redA02
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	4redB01
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	4redB02
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	119.532 Å
Unit-cell length b length_b	119.532 Å
Unit-cell length c length_c	215.639 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	29.900 Å
R factor r_factor	0.2331
R_work r_work	0.2297
R_free r_free	0.2768

fit	/app/data/saxs_computation/re/4red/4red.fit
pddf	/app/data/pr_computation/re/4red/4red.pr.out
profile	/app/data/saxs_computation/re/4red/4red.dat

Crystal structure of human AMPK alpha1 KD-AID with K43A mutation

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

;5'-AMP-activated protein kinase catalytic subunit alpha-1 ;

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