6y05

Crystal structure of the cAMP-dependent protein kinase A cocrystallized with adenine and PKI (5-24)

Method: X-RAY DIFFRACTION Dmax: 66.3 Å Quality: EXCELLENT

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

cAMP-dependent protein kinase catalytic subunit alpha

Cricetulus griseus

UniProt P25321

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 1–351 Non-standard monomer:Yes (specific site not provided by mmCIF) cAMP-dependent protein kinase inhibitor alpha × 1 (P63248) ADE ADENINE × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.9;277 K;100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 Mega 8, 10mM adenine in DMSO, 0.5 mM PKI (5-24) and 23 % methanol (v/v)0.004 mL drop volume, 0.5 mL reservoir volume Resolution 1.70 Å R-free 0.205

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.

158 other PDB entries and 158 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAPCA_CRIGR
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–353; UniProt 1–351

cAMP-dependent protein kinase inhibitor alpha

OrganismNot specified

UniProt P63248

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 B; UniProt 6–25 Not recorded cAMP-dependent protein kinase catalytic subunit alpha × 1 (P25321) ADE ADENINE × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.9;277 K;100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 Mega 8, 10mM adenine in DMSO, 0.5 mM PKI (5-24) and 23 % methanol (v/v)0.004 mL drop volume, 0.5 mL reservoir volume Resolution 1.70 Å R-free 0.205

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.

46 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IPKA_MOUSE
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; 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 6y05

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6y05
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6y05
Deposition date deposition_date2020-02-06
Structure title titleCrystal structure of the cAMP-dependent protein kinase A cocrystallized with adenine and PKI (5-24)
Keywords keywordsphosphotransferase, signalling pathways, glycogen metabolism, serine/threonine kinase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.59
Radius of gyration Rg (electron density) rg_electron20.18
Forward intensity I(0) i027197800.00
Molecular weight molecular_weight41173.0 kDa
Excluded volume excluded_volume52013 ų
Envelope volume envelope_volume59873 ų
Hydration-shell volume shell_volume24172 ų
Envelope diameter envelope_diameter68.5
Shell Rg shell_rg27.36
Envelope Rg envelope_rg20.36
Shape Rg shape_rg20.15
Total Rg total_rg21.21
Total atoms total_atoms2914
Residues n_residues360
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 dmax66.3
Rg (real space) rg_real21.44
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real2.7200e+07
I(0) uncertainty (real space) i0_real_error3.3800e+05
Rg (reciprocal space) rg_reciprocal21.47
I(0) (reciprocal space) i0_reciprocal27200000.0000
Solution quality estimate total_estimate0.9032
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3
Skewness Skewness skewness0.163
Kurtosis Kurtosis kurtosis-0.420
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7657000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)