6c0u

Crystal structure of cAMP-dependent protein kinase Calpha subunit bound with N46

Method: X-RAY DIFFRACTION Dmax: 67.9 Å Quality: EXCELLENT

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

cAMP-dependent protein kinase catalytic subunit alpha

Homo sapiens

UniProt P17612

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–351 Non-standard monomer:Yes (specific site not provided by mmCIF) EE4 N-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 3 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;16% (w/v) PEG8000, 0.04 M potassium phosphate (monobasic), 20% (v/v) glycerol Resolution 2.65 Å R-free 0.243

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.

53 other PDB entries and 78 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAPCA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–354; UniProt 1–351

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 6c0u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c0u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6c0u
Deposition date deposition_date2018-01-02
Structure title titleCrystal structure of cAMP-dependent protein kinase Calpha subunit bound with N46
Keywords keywordsSerine/threonine protein kinase (EC 2.7.11.11), TRANSFERASE, 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_guinier21.55
Radius of gyration Rg (electron density) rg_electron20.21
Forward intensity I(0) i024600500.00
Molecular weight molecular_weight38802.0 kDa
Excluded volume excluded_volume48828 ų
Envelope volume envelope_volume57121 ų
Hydration-shell volume shell_volume23188 ų
Envelope diameter envelope_diameter69.3
Shell Rg shell_rg27.31
Envelope Rg envelope_rg20.53
Shape Rg shape_rg20.20
Total Rg total_rg21.18
Total atoms total_atoms2742
Residues n_residues338
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 dmax67.9
Rg (real space) rg_real21.44
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real2.4600e+07
I(0) uncertainty (real space) i0_real_error2.6580e+05
Rg (reciprocal space) rg_reciprocal21.46
I(0) (reciprocal space) i0_reciprocal24600000.0000
Solution quality estimate total_estimate0.9017
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.9
Skewness Skewness skewness0.203
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5909000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6c0ua_
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_id6c0uA01
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_id6c0uA02
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)