7y1g

Crystal structure of human PRKACA complexed with DS01080522

Method: X-RAY DIFFRACTION Dmax: 91.2 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) I5G 1-chloranyl-~{N}-[(~{S})-(3-chloranyl-4-cyano-phenyl)-[(2~{R},4~{S})-4-oxidanylpyrrolidin-2-yl]methyl]-7-methoxy-isoquinoline-6-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.4;293 K;25 mM Tris, pH 8.4/ 20% PEG3350/ 0.05 M Zn Acetate/ 25 mM Glycine Resolution 2.30 Å R-free 0.237
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–351 Non-standard monomer:Yes (specific site not provided by mmCIF) I5G 1-chloranyl-~{N}-[(~{S})-(3-chloranyl-4-cyano-phenyl)-[(2~{R},4~{S})-4-oxidanylpyrrolidin-2-yl]methyl]-7-methoxy-isoquinoline-6-carboxamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.4;293 K;25 mM Tris, pH 8.4/ 20% PEG3350/ 0.05 M Zn Acetate/ 25 mM Glycine Resolution 2.30 Å R-free 0.237

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 77 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 1–351; UniProt 1–351 Author chain B; PDBConstruct 1–351; 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 7y1g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7y1g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7y1g
Deposition date deposition_date2022-06-08
Structure title titleCrystal structure of human PRKACA complexed with DS01080522
Keywords keywordsSERINE/THREONINE PROTEIN KINASE, protein kinase inhibitor, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.57
Radius of gyration Rg (electron density) rg_electron27.32
Forward intensity I(0) i090656800.00
Molecular weight molecular_weight77435.0 kDa
Excluded volume excluded_volume97884 ų
Envelope volume envelope_volume118910 ų
Hydration-shell volume shell_volume35986 ų
Envelope diameter envelope_diameter92.6
Shell Rg shell_rg35.05
Envelope Rg envelope_rg27.22
Shape Rg shape_rg27.28
Total Rg total_rg28.26
Total atoms total_atoms5475
Residues n_residues669
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 dmax91.2
Rg (real space) rg_real28.51
Rg uncertainty (real space) rg_real_error0.40
I(0) (real space) i0_real9.0660e+07
I(0) uncertainty (real space) i0_real_error1.2610e+06
Rg (reciprocal space) rg_reciprocal28.54
I(0) (reciprocal space) i0_reciprocal90660000.0000
Solution quality estimate total_estimate0.9007
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.2
Skewness Skewness skewness0.275
Kurtosis Kurtosis kurtosis-0.445
Angular range angular_range— – 0.2800 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha22710000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.960

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id7y1gA01
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_id7y1gB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)