SAXSdb — 2f15

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

;5'-AMP-activated protein kinase, beta-2 subunit ;

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 69–163	Fragment：Glycogen-Binding Domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；27% MPD, 0.1 M Hepes, pH 7.5, 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.296

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 2F15	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V8Q Crystal structure of the regulatory fragment of mammalian AMPK in complexes with AMP Deposited 2007-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 187–272（86 aa） Fragment：RESIDUES 187-272	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.237
2V92 Crystal structure of the regulatory fragment of mammalian AMPK in complexes with ATP-AMP Deposited 2007-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 187–272（86 aa） Fragment：RESIDUES 187-272	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.259
2V9J Crystal structure of the regulatory fragment of mammalian AMPK in complexes with Mg.ATP-AMP Deposited 2007-08-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 187–272（86 aa） Fragment：RESIDUES 187-272	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.53 Å R-free 0.266
2Y8L Structure of the regulatory fragment of mammalian aMPK in complex with two ADP Deposited 2011-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 187–272（86 aa） Fragment：RESIDUES 187-272	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.253
2Y8Q Structure of the regulatory fragment of mammalian AMPK in complex with one ADP Deposited 2011-02-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 187–272（86 aa） Fragment：RESIDUES 187-272	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.275
2YA3 STRUCTURE OF THE REGULATORY FRAGMENT OF MAMMALIAN AMPK IN COMPLEX WITH COUMARIN ADP Deposited 2011-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 187–272（86 aa） Fragment：RESIDUES 187-272	Not recorded	J7V 3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxy-ADP × 2 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.51 Å R-free 0.263
4CFH Structure of an active form of mammalian AMPK Deposited 2013-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 187–272（86 aa） Fragment：RESIDUES 187-272	Not recorded	STU STAUROSPORINE × 1 AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；CRYSTALS WERE GROWN BY THE HANGING DROP METHOD WITH RESERVOIR SOLUTION CONTAINING 8% ISOPROPANOL AND 5% MPD AS PRECIPITANT IN 0.1M TRIS AT PH 7.5 AT 18 DEGREES.	Resolution 3.24 Å R-free 0.268
4EAI Co-crystal structure of an AMPK core with AMP Deposited 2012-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 189–272（84 aa） Fragment：UNP residues 189-272	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.26；298 K；MES, 16% IPP, 1% 1,4-butanediol, pH 6.26, VAPOR DIFFUSION, HANGING DROP, temperature 298 K	Resolution 2.29 Å R-free 0.252
4EAJ Co-crystal of AMPK core with AMP soaked with ATP Deposited 2012-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 189–272（84 aa） Fragment：UNP residues 189-272	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.26；298 K；MES pH 6.26, 16% IPP, 1% 1,4-butanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298 K	Resolution 2.61 Å R-free 0.258
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 B 76–272（197 aa） Fragment：Human AMPK beta2 subunit [A76-I272]	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 76–272（197 aa） Fragment：Human AMPK beta2 subunit [A76-I272]	Not recorded	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
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 B 1–272（272 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
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 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 B 75–272（198 aa）	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 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 B 75–272（198 aa）	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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 76–272（197 aa）	Not recorded	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
7M74 ATP-bound AMP-activated protein kinase Deposited 2021-03-26	Different construct 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 B 76–272（197 aa）	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 3.93 Å

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AAKB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–96； UniProt 69–163

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	2f15
Deposition date deposition_date	2005-11-14
Structure title title	Glycogen-Binding Domain Of The Amp-Activated Protein Kinase beta2 Subunit
Keywords keywords	;BETA SANDWICH, FATTY ACID BIOSYNTHESIS, LIPID SYNTHESIS, PHOSPHORYLATION, STRUCTURAL GENOMICS CONSORTIUM, SGC, SUGAR BINDING PROTEIN ;; SUGAR BINDING PROTEIN
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	14.78 Å
Radius of gyration Rg (electron density) rg_electron	13.79 Å
Forward intensity I(0) i0	2083480.00
Molecular weight molecular_weight	10134.0 kDa
Excluded volume excluded_volume	12794 Å³
Envelope volume envelope_volume	14867 Å³
Hydration-shell volume shell_volume	9835 Å³
Envelope diameter envelope_diameter	51.8 Å
Shell Rg shell_rg	18.59 Å
Envelope Rg envelope_rg	14.38 Å
Shape Rg shape_rg	13.79 Å
Total Rg total_rg	14.94 Å
Total atoms total_atoms	721
Residues n_residues	89
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	53.8 Å
Rg (real space) rg_real	14.77 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.0830e+06
I(0) uncertainty (real space) i0_real_error	2.4140e+04
Rg (reciprocal space) rg_reciprocal	14.77 Å
I(0) (reciprocal space) i0_reciprocal	2083000.0000
Solution quality estimate total_estimate	0.8450
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.0 Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.155
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	284500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.693; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.906; Smooth: 0.998

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2f15a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.21 — AMPK-beta glycogen binding domain-like

CATH v4.4 (1 domains)

Domain ID domain_id	2f15A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	69.723 Å
Unit-cell length b length_b	69.723 Å
Unit-cell length c length_c	118.491 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.750 Å
R factor r_factor	0.2392
R_work r_work	0.2366
R_free r_free	0.2961

Description description	;5'-AMP-activated protein kinase, beta-2 subunit ;
Molecular weight formula_weight	10865.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	754

Glycogen-Binding Domain Of The Amp-Activated Protein Kinase beta2 Subunit

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

;5'-AMP-activated protein kinase, beta-2 subunit ;

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 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	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

fit	/app/data/saxs_computation/f1/2f15/2f15.fit
pddf	/app/data/pr_computation/f1/2f15/2f15.pr.out
profile	/app/data/saxs_computation/f1/2f15/2f15.dat