4wb8

Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit), exon 1 deletion

Method: X-RAY DIFFRACTION Dmax: 66.9 Å Quality: GOOD

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 16–351 Fragment:UNP residues 16-351 Mutation:none Non-standard monomer:Yes (specific site not provided by mmCIF) PKI (5-24) × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;295 K;10% PEG 8000, 0.1M HEPES pH 7.5 Resolution 1.55 Å R-free 0.184

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 2–337; UniProt 16–351

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 4wb8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4wb8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4wb8
Deposition date deposition_date2014-09-02
Structure title titleCrystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit), exon 1 deletion
Keywords keywordscatalysis, protein kinase, adenosine triphosphate, phosphorylation, 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_guinier21.24
Radius of gyration Rg (electron density) rg_electron20.02
Forward intensity I(0) i029670300.00
Molecular weight molecular_weight42409.0 kDa
Excluded volume excluded_volume53293 ų
Envelope volume envelope_volume60641 ų
Hydration-shell volume shell_volume24403 ų
Envelope diameter envelope_diameter70.3
Shell Rg shell_rg27.45
Envelope Rg envelope_rg20.38
Shape Rg shape_rg19.99
Total Rg total_rg21.06
Total atoms total_atoms2989
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 dmax66.9
Rg (real space) rg_real21.10
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real2.9670e+07
I(0) uncertainty (real space) i0_real_error3.5680e+05
Rg (reciprocal space) rg_reciprocal21.13
I(0) (reciprocal space) i0_reciprocal29670000.0000
Solution quality estimate total_estimate0.8945
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary64.9
Skewness Skewness skewness0.184
Kurtosis Kurtosis kurtosis-0.378
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8676000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4wb8A01
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_id4wb8A02
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)