SAXSdb — 2hwn

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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 0–44 Chain B； UniProt 0–44	Fragment：Dimerization/docking domain, residues 0-44	A Kinase binding peptide × 1 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 0–44 Chain D； UniProt 0–44	Fragment：Dimerization/docking domain, residues 0-44	A Kinase binding peptide × 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
3	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 0–44 Chain B； UniProt 0–44 Chain C； UniProt 0–44 Chain D； UniProt 0–44	Fragment：Dimerization/docking domain, residues 0-44	A Kinase binding peptide × 2 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

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 2HWN	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	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	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
2H9R 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) Deposited 2006-06-10	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	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
2IZY Molecular Basis of AKAP Specificity for PKA Regulatory Subunits Deposited 2006-07-27	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 4 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 1–45； UniProt 0–44 Author chain B； PDBConstruct 1–45； UniProt 0–44 Author chain C； PDBConstruct 1–45； UniProt 0–44 Author chain D； PDBConstruct 1–45； UniProt 0–44

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	2hwn
Deposition date deposition_date	2006-08-01
Structure title title	Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide
Keywords keywords	PKA, AKAP, Dimerization/Docking, D/D, Regulatory Subunit, 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	21.58 Å
Radius of gyration Rg (electron density) rg_electron	20.82 Å
Forward intensity I(0) i0	8967950.00
Molecular weight molecular_weight	23189.0 kDa
Excluded volume excluded_volume	29462 Å³
Envelope volume envelope_volume	35949 Å³
Hydration-shell volume shell_volume	15308 Å³
Envelope diameter envelope_diameter	72.5 Å
Shell Rg shell_rg	25.71 Å
Envelope Rg envelope_rg	20.76 Å
Shape Rg shape_rg	20.78 Å
Total Rg total_rg	21.72 Å
Total atoms total_atoms	1637
Residues n_residues	206
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	74.4 Å
Rg (real space) rg_real	21.68 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	8.9680e+06
I(0) uncertainty (real space) i0_real_error	1.3600e+05
Rg (reciprocal space) rg_reciprocal	21.67 Å
I(0) (reciprocal space) i0_reciprocal	8968000.0000
Solution quality estimate total_estimate	0.8478
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.8 Å
Skewness Skewness skewness	0.416
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1940000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.810; Smooth: 0.936

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	cAMP-dependent protein kinase type II-alpha regulatory subunit
Molecular weight formula_weight	5290.1 kDa
EC 编号 ec_number	2.7.11.11
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1853

MSHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	A Kinase binding peptide
Molecular weight formula_weight	2611.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

QEELAWKIAKMIVSDVMQQCKK

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	211

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2hwna_
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	d2hwnb_
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	d2hwnc_
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	d2hwnd_
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

CATH v4.4 (3 domains)

Domain ID domain_id	2hwnB00
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	2hwnC00
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	2hwnD00
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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Unit-cell length a length_a	99.551 Å
Unit-cell length b length_b	44.561 Å
Unit-cell length c length_c	72.802 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.500 Å
R factor r_factor	0.2082
R_work r_work	0.2080
R_free r_free	0.2390

fit	/app/data/saxs_computation/hw/2hwn/2hwn.fit
pddf	/app/data/pr_computation/hw/2hwn/2hwn.pr.out
profile	/app/data/saxs_computation/hw/2hwn/2hwn.dat

Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide

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

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)