3dnd

cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24

Method: X-RAY DIFFRACTION Dmax: 66.4 Å Quality: EXCELLENT

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

cAMP-dependent protein kinase catalytic subunit alpha

Bos taurus

UniProt P00517

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–351 Non-standard monomer:Yes (specific site not provided by mmCIF) cAMP-dependent protein kinase inhibitor alpha × 1 (P61926) LL2 5-benzyl-1,3-thiazol-2-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;277 K;75mM LiCl, 30mM MesBisTris, 1mM DTT, 0.2mM EDTA, pH 6.5, 15% Methanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.26 Å R-free 0.253

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.

97 other PDB entries and 111 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAPCA_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–350; UniProt 2–351

cAMP-dependent protein kinase inhibitor alpha

OrganismNot specified

UniProt P61926

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain I; UniProt 6–25 Fragment:Inhibitory Fragment, UNP residues 6-25 cAMP-dependent protein kinase catalytic subunit alpha × 1 (P00517) LL2 5-benzyl-1,3-thiazol-2-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;277 K;75mM LiCl, 30mM MesBisTris, 1mM DTT, 0.2mM EDTA, pH 6.5, 15% Methanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.26 Å R-free 0.253

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IPKA_RABIT
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–20; UniProt 6–25

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 3dnd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dnd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3dnd
Deposition date deposition_date2008-07-02
Structure title titlecAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24
Keywords keywords;ATP-binding, Kinase, Lipoprotein, Myristate, Nucleotide-binding, Nucleus, Phosphoprotein, Serine/threonine-protein kinase, Transferase, cAMP, Protein kinase inhibitor, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX ;; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.61
Radius of gyration Rg (electron density) rg_electron20.26
Forward intensity I(0) i027942100.00
Molecular weight molecular_weight41739.0 kDa
Excluded volume excluded_volume52771 ų
Envelope volume envelope_volume61008 ų
Hydration-shell volume shell_volume24480 ų
Envelope diameter envelope_diameter68.8
Shell Rg shell_rg27.46
Envelope Rg envelope_rg20.44
Shape Rg shape_rg20.22
Total Rg total_rg21.34
Total atoms total_atoms2950
Residues n_residues354
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax66.4
Rg (real space) rg_real21.47
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real2.7940e+07
I(0) uncertainty (real space) i0_real_error3.3030e+05
Rg (reciprocal space) rg_reciprocal21.49
I(0) (reciprocal space) i0_reciprocal27940000.0000
Solution quality estimate total_estimate0.9009
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.3
Skewness Skewness skewness0.167
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8481000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.980

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3dnda_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id3dndA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id3dndA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1

8. Citations (1)

9. Files and Curves (10)