SAXSdb — 2h9r

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

cAMP-dependent protein kinase type II-alpha regulatory subunit

Rattus norvegicus

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 2–44 Chain B； UniProt 2–44	Fragment：N-terminal docking and dimerization domain, residues 4-46	22-mer from A-kinase anchor protein 5 × 1 （P24588）	SOLUTION NMR NMR measurement conditions：pH 4；298 K；Pressure 1 NMR sample composition：2mM RII-alpha(1-44); 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2H9R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DRN Docking and dimerization domain (D/D) of the Type II-alpha regulatory subunity of protein kinase A (PKA) in complex with a peptide from an A-kinase anchoring protein Deposited 2006-06-11	Parsed fields agree	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 2–44（43 aa） Fragment：N-terminal docking and dimerization domain, residues 4-46 Chain B 2–44（43 aa） Fragment：N-terminal docking and dimerization domain, residues 4-46	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Pressure 1 NMR sample composition 2mM RII-alpha(1-44); 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2HWN Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide Deposited 2006-08-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain B 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100mM HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.239
2HWN Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide Deposited 2006-08-01	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain D 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100mM HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.239
2HWN Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide Deposited 2006-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain B 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain C 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44 Chain D 0–44（45 aa） Fragment：Dimerization/docking domain, residues 0-44	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；100mM HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.239
2IZY Molecular Basis of AKAP Specificity for PKA Regulatory Subunits Deposited 2006-07-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 2–44（43 aa） Fragment：RESIDUES 2-44 Chain B 2–44（43 aa） Fragment：RESIDUES 2-44 Chain C 2–44（43 aa） Fragment：RESIDUES 2-44 Chain D 2–44（43 aa） Fragment：RESIDUES 2-44 Chain E 2–44（43 aa） Fragment：RESIDUES 2-44 Chain F 2–44（43 aa） Fragment：RESIDUES 2-44 Chain G 2–44（43 aa） Fragment：RESIDUES 2-44 Chain H 2–44（43 aa） Fragment：RESIDUES 2-44	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；8-10% PEG400, 0.2-0.4 M SODIUM PHOSPHATE AND SODIUM CITRATE (PH 5.8)	Resolution 2.20 Å R-free 0.272
3TMH Crystal structure of dual-specific A-kinase anchoring protein 2 in complex with cAMP-dependent protein kinase A type II alpha and PDZK1 Deposited 2011-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain B 1–45（45 aa） Fragment：Dimerization/docking domain (D/D), UNP RESIDUES 3-44 Chain C 1–45（45 aa） Fragment：Dimerization/docking domain (D/D), UNP RESIDUES 3-44 Chain F 1–45（45 aa） Fragment：Dimerization/docking domain (D/D), UNP RESIDUES 3-44 Chain G 1–45（45 aa） Fragment：Dimerization/docking domain (D/D), UNP RESIDUES 3-44	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7；293 K；100 mM HEPES, pH 7, 20% PEG MME, Microbatch, temperature 293K	Resolution 3.80 Å R-free 0.328

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KAP2_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–46； UniProt 2–44 Author chain B； PDBConstruct 4–46； UniProt 2–44

22-mer from A-kinase anchor protein 5

OrganismNot specified

UniProt P24588

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 391–412	Fragment：PKA-RII subunit binding domain	cAMP-dependent protein kinase type II-alpha regulatory subunit × 2 （P12368）	SOLUTION NMR NMR measurement conditions：pH 4；298 K；Pressure 1 NMR sample composition：2mM RII-alpha(1-44); 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2H9R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3LL8 Crystal Structure of Calcineurin in Complex with AKAP79 Peptide Deposited 2010-01-28	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 336–346（11 aa） Fragment：UNP residues 336-346	Not recorded	PO4 PHOSPHATE ION × 1 ZN ZINC ION × 1 FE FE (III) ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 20,000 MgSO4 CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.228
3LL8 Crystal Structure of Calcineurin in Complex with AKAP79 Peptide Deposited 2010-01-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 336–346（11 aa） Fragment：UNP residues 336-346	Not recorded	PO4 PHOSPHATE ION × 2 ZN ZINC ION × 2 FE FE (III) ION × 2 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 20,000 MgSO4 CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.228
5NIN Crystal Structure of AKAP79 calmodulin binding domain peptide in complex with Ca2+/Calmodulin Deposited 2017-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 77–92（16 aa） Fragment：UNP residues 77-92	Not recorded	CA CALCIUM ION × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；287 K；2.4 M ammonium sulphate, 50 mM citrate pH 5.4, 0.3 M NDSB-195	Resolution 1.70 Å R-free 0.194
5NIN Crystal Structure of AKAP79 calmodulin binding domain peptide in complex with Ca2+/Calmodulin Deposited 2017-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 77–92（16 aa） Fragment：UNP residues 77-92	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；287 K；2.4 M ammonium sulphate, 50 mM citrate pH 5.4, 0.3 M NDSB-195	Resolution 1.70 Å R-free 0.194

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AKAP5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–22； UniProt 391–412

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	2h9r
Deposition date deposition_date	2006-06-10
Structure title title	Docking and dimerization domain (D/D) of the regulatory subunit of the Type II-alpha cAMP-dependent protein kinase A associated with a Peptide derived from an A-kinase anchoring protein (AKAP)
Keywords keywords	AKAP, PKA, signal transduction, 4-helix bundle, helix-loop-helix, protein-peptide complex, TRANSFERASE; TRANSFERASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.75 Å
Radius of gyration Rg (electron density) rg_electron	15.70 Å
Forward intensity I(0) i0	234567000.00
Molecular weight molecular_weight	131620.0 kDa
Excluded volume excluded_volume	166610 Å³
Envelope volume envelope_volume	42132 Å³
Hydration-shell volume shell_volume	18652 Å³
Envelope diameter envelope_diameter	70.4 Å
Shell Rg shell_rg	25.26 Å
Envelope Rg envelope_rg	19.98 Å
Shape Rg shape_rg	15.62 Å
Total Rg total_rg	16.37 Å
Total atoms total_atoms	16190
Residues n_residues	1140
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	66.6 Å
Rg (real space) rg_real	16.75 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	2.3460e+08
I(0) uncertainty (real space) i0_real_error	3.2790e+06
Rg (reciprocal space) rg_reciprocal	16.75 Å
I(0) (reciprocal space) i0_reciprocal	234600000.0000
Solution quality estimate total_estimate	0.6749
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.388
Kurtosis Kurtosis kurtosis	0.081
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	489200.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.334; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.767; Smooth: 0.000

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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	cAMP-dependent protein kinase type II-alpha regulatory subunit
Molecular weight formula_weight	5398.2 kDa
EC 编号 ec_number	2.7.1.37
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	16190

HMGHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	22-mer from A-kinase anchor protein 5
Molecular weight formula_weight	2383.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

LLIETASSLVKNAIQLSIEQLV

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2h9ra1
Class class	a — All alpha proteins
Fold Fold fold	a.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamily	a.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family family	a.31.1.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit

Domain ID domain_id	d2h9ra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2h9rb1
Class class	a — All alpha proteins
Fold Fold fold	a.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamily	a.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family family	a.31.1.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit

Domain ID domain_id	d2h9rb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2h9rA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

Domain ID domain_id	2h9rB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily	10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain

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8. Citations (1)

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fit	/app/data/saxs_computation/h9/2h9r/2h9r.fit
pddf	/app/data/pr_computation/h9/2h9r/2h9r.pr.out
profile	/app/data/saxs_computation/h9/2h9r/2h9r.dat

Docking and dimerization domain (D/D) of the regulatory subunit of the Type II-alpha cAMP-dependent protein kinase A associated with a Peptide derived from an A-kinase anchoring protein (AKAP)

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

cAMP-dependent protein kinase type II-alpha regulatory subunit

State in the Current Structure

Other States of the Same Protein in the Database

22-mer from A-kinase anchor protein 5

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)