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1l6e

Solution structure of the docking and dimerization domain of protein kinase A II-alpha (RIIalpha D/D). Alternatively called the N-terminal dimerization domain of the regulatory subunit of protein kinase A.

Method: SOLUTION NMR Dmax: 61.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

cAMP-dependent protein kinase Type II-alpha regulatory chain

Mus musculus

UniProt P12367

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 2–43 Chain B； UniProt 2–43 Fragment：N-terminal docking and dimerization domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 4；298 K；Ionic strength (raw mmCIF value) 0.012；Pressure 1 NMR measurement conditions：pH 4；298 K；Ionic strength (raw mmCIF value) 0.012；Pressure 1 NMR measurement conditions：pH 4；298 K；Ionic strength (raw mmCIF value) 0.012；Pressure 1 NMR measurement conditions：pH 4；298 K；Ionic strength (raw mmCIF value) 0.012；Pressure 1 NMR sample composition：2mM dimer protein in 20 mM sodium phosphate buffer, 90%H2O-10% D2O, at pH 4 and temperature 298K | 90% H2O/10% D2O NMR sample composition：1mM dimer protein 15N in 20 mM sodium phosphate buffer, 90%H2O-10% D2O, at pH 4 and temperature 298K | 90% H2O/10% D2O NMR sample composition：1mM dimer protein 13C-15N in 20 mM sodium phosphate buffer, 90%H2O-10% D2O, at pH 4 and temperature 298K | 90% H2O/10% D2O NMR sample composition：Mixture of 2mM unlabeled and 2 mM 13C-15N labeled sample unfolded in 5 M guanadine hydrochloride and refolded in 20 mM sodium phosphate buffer, 90% H2O-10% D2O, at pH 4 and temperature 298K | 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 1L6E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1R2A THE MOLECULAR BASIS FOR PROTEIN KINASE A ANCHORING REVEALED BY SOLUTION NMR Deposited 1998-12-07 Different construct Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–44（44 aa） Fragment：DIMERIZATION-ANCHORING DOMAIN
Chain B 1–44（44 aa） Fragment：DIMERIZATION-ANCHORING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4；298 K；Ionic strength (raw mmCIF value) 0.012 mM；Pressure 1
Resolution not provided
2QVS Crystal Structure of Type IIa Holoenzyme of cAMP-dependent Protein Kinase Deposited 2007-08-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 92–401（310 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295.5 K；1.9 M sodium formate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K
Resolution 2.50 Å R-free 0.251
9D2F 3D structure and atomic model of RS3 of mouse respiratory cilia Deposited 2024-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain b 1–401（401 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；30 mM HEPES pH 7.4, 25 mM KCl, 5 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE；4 microliters of splayed axoneme sample were applied to glow-discharged Quantifoil R2/2 Cu grids. After removing excess liquid by blotting the grid from the backside with Whatman filter paper for 2-3 s, the grid was immediately plunge-frozen in liquid ethane using a home-made plunge freezer.
Resolution 4.70 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAP2_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–46； UniProt 2–43 Author chain B； PDBConstruct 4–46； UniProt 2–43

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1l6e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1l6e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1l6e
Deposition date deposition_date2002-03-08
Structure title titleSolution structure of the docking and dimerization domain of protein kinase A II-alpha (RIIalpha D/D). Alternatively called the N-terminal dimerization domain of the regulatory subunit of protein kinase A.
Keywords keywordsFour-helix bundle, helix-loop-helix, regulatory subunit, dimerization, docking, anchoring, TRANSFERASE; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.33 Å
Radius of gyration Rg (electron density) rg_electron14.32 Å
Forward intensity I(0) i0912519000.00
Molecular weight molecular_weight258730.0 kDa
Excluded volume excluded_volume325440 ų
Envelope volume envelope_volume54785 ų
Hydration-shell volume shell_volume22368 ų
Envelope diameter envelope_diameter64.9 Å
Shell Rg shell_rg27.03 Å
Envelope Rg envelope_rg20.48 Å
Shape Rg shape_rg14.25 Å
Total Rg total_rg14.91 Å
Total atoms total_atoms36624
Residues n_residues2208
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax61.2 Å
Rg (real space) rg_real15.32 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real9.1250e+08
I(0) uncertainty (real space) i0_real_error1.1370e+07
Rg (reciprocal space) rg_reciprocal15.32 Å
I(0) (reciprocal space) i0_reciprocal912500000.0000
Solution quality estimate total_estimate0.7547
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.0 Å
Skewness Skewness skewness0.350
Kurtosis Kurtosis kurtosis-0.030
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha330800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.359; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.729; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1l6ea1
Class classa — All alpha proteins
Fold Fold folda.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamilya.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family familya.31.1.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Domain ID domain_idd1l6ea2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1l6eb1
Class classa — All alpha proteins
Fold Fold folda.31 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily Superfamily superfamilya.31.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family Family familya.31.1.1 — Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Domain ID domain_idd1l6eb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id1l6eA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain
Domain ID domain_id1l6eB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology890 — cAMP-dependent Protein Kinase, Chain A
Homologous superfamily homologous superfamily10 — cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain
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8. Citations (3)

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9. Files and Curves (10)