SAXSdb — 9pln

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

Alpha-2A adrenergic receptor

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 R； UniProt 2–465	Not recorded	A1CIU N-(5-methylnaphthalen-1-yl)pyridin-4-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；CHS was solubilized in LMNG and GDN prior to diluting into buffers. cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.80 Å

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 9PLN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HLL NMR STRUCTURE OF T3-I2, A 32 RESIDUE PEPTIDE FROM THE ALPHA-2A ADRENERGIC RECEPTOR Deposited 2000-12-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–149（32 aa） Fragment：SECOND INTRACELLULAR LOOP T3-I2 (RESIDUES 118-149)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM NaCl NMR sample composition 0.9 mM T3-I2 natural abundance; 460 mM D38-dodecylphosphocholine, 50 mM NaCl, 10 mM NaH2PO4, pH 4.5 \| 90% H2O/10% D2O NMR sample composition 0.9 mM T3-I2 natural abundance; 460 mM D38 dodecylphosphocholine, 50 mM NaCl, 10 mM NaH2PO4, pH 4.5 \| 100% D2O	Resolution not provided
1HO9 BEST 20 NMR CONFORMERS OF D130I MUTANT T3-I2, A 32 RESIDUE PEPTIDE FROM THE ALPHA 2A ADRENERGIC RECEPTOR Deposited 2000-12-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–149（32 aa） Fragment：SECOND INTRACELLULAR LOOP (RESIDUES 118-149)	Mutation：D130I	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM NACL NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM NMR sample composition 0.9 mM PEPTIDE NATURAL ABUNDANCE; 460 mM D38- DODECYLPHOSPHOCHOLINE, 50 mM NACL, 10 mM NAH2PO4, PH 4.5 \| 90% H2O/10% D2O NMR sample composition 0.9 mM PEPTIDE NATURAL ABUNDANCE; 460 mM D38- DODECYLPHOSPHOCHOLINE, 50 mM NACL, 10 mM NAH2PO4, PH 4.5 \| 100% D20	Resolution not provided
1HOD NMR STRUCTURE OF D130I MUTANT T3-I2, A 32 RESIDUE PEPTIDE FROM THE ALPHA 2A ADRENERGIC RECEPTOR Deposited 2000-12-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–149（32 aa） Fragment：SECOND INTRACELLULAR LOOP (RESIDUES 118-149)	Mutation：D130I	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM NACL NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM NMR sample composition 0.9 mM PEPTIDE NATURAL ABUNDANCE; 460 mM D38- DODECYLPHOSPHOCHOLINE, 50 mM NACL, 10 mM NAH2PO4, PH 4.5 \| 90% H2O/10% D2O NMR sample composition 0.9 mM PEPTIDE NATURAL ABUNDANCE; 460 mM D38- DODECYLPHOSPHOCHOLINE, 50 mM NACL, 10 mM NAH2PO4, PH 4.5 \| 100 % D20	Resolution not provided
1HOF NMR STRUCTURE OF T3-I2, A 32 RESIDUE PEPTIDE FROM THE ALPHA-2A ADRENERGIC RECEPTOR Deposited 2000-12-10	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–149（32 aa） Fragment：SECOND INTRACELLULAR LOOP (RESIDUES 118-149)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM NACL NMR measurement conditions pH 4.5；303 K；Ionic strength (raw mmCIF value) 50 mM NMR sample composition 0.9 MM T3-I2 PEPTIDE NATURAL ABUNDANCE; 460 mM D38- DODECYLPHOSPHOCHOLINE, 50 mM NACL, 10 mM NAH2PO4, PH 4.5 \| 90% H2O/10% D2O NMR sample composition 0.9 MM T3-I2 PEPTIDE NATURAL ABUNDANCE; 460 mM D38- DODECYLPHOSPHOCHOLINE, 50 mM NACL, 10 mM NAH2PO4, PH 4.5 \| 100% D2O	Resolution not provided
6K42 cryo-EM structure of alpha2BAR-Gi1 complex Deposited 2019-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–27（27 aa）	Not recorded	CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7EJ0 Structure of the alpha2A-adrenergic receptor GoA signaling complex Deposited 2021-04-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–465（465 aa）	Not recorded	E5E Noradrenaline × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7EJ8 Structure of the alpha2A-adrenergic receptor GoA signaling complex bound to brimonidine Deposited 2021-04-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–465（465 aa）	Not recorded	J59 Brimonidine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7EJA Structure of the alpha2A-adrenergic receptor GoA signaling complex bound to dexmedetomidine Deposited 2021-04-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–465（465 aa）	Not recorded	CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7EJK Structure of the alpha2A-adrenergic receptor GoA signaling complex bound to oxymetazoline Deposited 2021-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–465（465 aa）	Not recorded	J5C Oxymetazoline × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7W6P Cryo-EM structure of the alpha2A adrenergic receptor GoA signaling complex bound to a G protein biased agonist Deposited 2021-12-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–465（465 aa）	Not recorded	W96 N-pyridin-4-ylisoquinolin-4-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
7W7E Cryo-EM structure of the alpha2A adrenergic receptor GoA signaling complex bound to a biased agonist Deposited 2021-12-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–465（465 aa）	Not recorded	W58 5-(3-bicyclo[4.2.0]octa-1,3,5-trienyl)-1,2,3,6-tetrahydropyridine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9CBL Cryo-EM structure of epinephrine-bound alpha-2A-adrenergic receptor in complex with heterotrimeric Gi-protein Deposited 2024-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 35–242（208 aa） Chain R 380–460（81 aa）	Not recorded	ALE L-EPINEPHRINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9CBM Cryo-EM structure of dexmedetomidine-bound alpha-2A-adrenergic receptor in complex with heterotrimeric Gi-protein Deposited 2024-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 35–242（208 aa） Chain R 380–460（81 aa）	Not recorded	CZX 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9IQR Cryo-EM structure of MT3-alpha2AAR Deposited 2024-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 38–241（204 aa） Chain B 379–456（78 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.40 Å
9PLO Structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and N-(5-methylnaphthalen-1-yl)pyridin-4-amine (compound 4905) Deposited 2025-07-15	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–465（464 aa）	Not recorded	A1CIU N-(5-methylnaphthalen-1-yl)pyridin-4-amine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；CHS was solubilized in LMNG and GDN prior to diluting into buffers. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.74 Å
9PQD Locally-refined structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and compound Z7149 Deposited 2025-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 2–465（464 aa）	Not recorded	A1CIZ (6M)-1-methyl-6-(1,2,5,6-tetrahydropyridin-3-yl)-1H-indole × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer was supplemented with 0.01 mM compound Z7149 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å

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

View Construct and Data Evidence

UniProt name	ADA2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain R； PDBConstruct 28–491； UniProt 2–465

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	9pln
Deposition date deposition_date	2025-07-15
Structure title title	Locally-refined structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and N-(5-methylnaphthalen-1-yl)pyridin-4-amine (compound 4905)
Keywords keywords	Receptor, Drug, Complex, GPCR, G-protein, scFv16, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.90 Å
Radius of gyration Rg (electron density) rg_electron	19.94 Å
Forward intensity I(0) i0	25929300.00
Molecular weight molecular_weight	27810.0 kDa
Excluded volume excluded_volume	27918 Å³
Envelope volume envelope_volume	44879 Å³
Hydration-shell volume shell_volume	19272 Å³
Envelope diameter envelope_diameter	72.1 Å
Shell Rg shell_rg	26.09 Å
Envelope Rg envelope_rg	20.37 Å
Shape Rg shape_rg	19.88 Å
Total Rg total_rg	20.74 Å
Total atoms total_atoms	2136
Residues n_residues	266
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	71.0 Å
Rg (real space) rg_real	20.89 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	2.5930e+07
I(0) uncertainty (real space) i0_real_error	3.7440e+05
Rg (reciprocal space) rg_reciprocal	20.89 Å
I(0) (reciprocal space) i0_reciprocal	25930000.0000
Solution quality estimate total_estimate	0.8728
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.358
Kurtosis Kurtosis kurtosis	-0.280
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2348000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.957

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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	Alpha-2A adrenergic receptor
Molecular weight formula_weight	53643.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R
Atom count atom_count	2136

MKTIIALSYIFCLVFADYKDDDDASIDFRQEQPLAEGSFAPMGSLQPDAGNASWNGTEAPGGGARATPYSLQVTLTLVCLAGLLMLLTVFGNVLVIIAVFTSRALKAPQNLFLVSLASADILVATLVIPFSLANEVMGYWYFGKAWCEIYLALDVLFCTSSIVHLCAISLDRYWSITQAIEYNLKRTPRRIKAIIITVWVISAVISFPPLISIEKKGGGGGPQPAEPRCEINDQKWYVISSCIGSFFAPCLIMILVYVRIYQIAKRRTRVPPSRRGPDAVAAPPGGTERRPNGLGPERSAGPGGAEAEPLPTQLNGAPGEPAPAGPRDTDALDLEESSSSDHAERPPGPRRPERGPRGKGKARASQVKPGDSLPRRGPGATGIGTPAAGPGEERVGAAKASRWRGRQNREKRFTFVLAVVIGVFVVCWFPFFFTYTLTAVGCSVPRTLFKFFFWFGYCNSSLNPVIYTIFNHDFRRAFKKILCRGDRKRIV

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	N-(5-methylnaphthalen-1-yl)pyridin-4-amine
Molecular weight formula_weight	234.3 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	323827

fit	/app/data/saxs_computation/pl/9pln/9pln.fit
pddf	/app/data/pr_computation/pl/9pln/9pln.pr.out
profile	/app/data/saxs_computation/pl/9pln/9pln.dat

Locally-refined structure of alpha2a adrenergic receptor in complex with Go heterotrimer, scFv16, and N-(5-methylnaphthalen-1-yl)pyridin-4-amine (compound 4905)

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

Alpha-2A adrenergic receptor

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)