2f7z

Protein Kinase A bound to (R)-1-(1H-Indol-3-ylmethyl)-2-(2-pyridin-4-yl-[1,7]naphtyridin-5-yloxy)-ehylamine

Method: X-RAY DIFFRACTION Dmax: 65.5 Å Quality: GOOD

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

cAMP-dependent protein kinase, alpha-catalytic subunit

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 E; UniProt 0–350 Not recorded PKI, inhibitory peptide × 1 6EA (1S)-1-(1H-INDOL-3-YLMETHYL)-2-(2-PYRIDIN-4-YL-[1,7]NAPHTYRIDIN-5-YLOXY)-EHYLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.00 Å R-free 0.342

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 E; PDBConstruct 1–351; UniProt 0–350

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 2f7z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2f7z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2f7z
Deposition date deposition_date2005-12-01
Structure title titleProtein Kinase A bound to (R)-1-(1H-Indol-3-ylmethyl)-2-(2-pyridin-4-yl-[1,7]naphtyridin-5-yloxy)-ehylamine
Keywords keywordsProtein Kinase A, AKT inhibitors, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.32
Radius of gyration Rg (electron density) rg_electron20.03
Forward intensity I(0) i027368100.00
Molecular weight molecular_weight41754.0 kDa
Excluded volume excluded_volume52919 ų
Envelope volume envelope_volume59419 ų
Hydration-shell volume shell_volume24110 ų
Envelope diameter envelope_diameter68.5
Shell Rg shell_rg27.20
Envelope Rg envelope_rg20.20
Shape Rg shape_rg19.99
Total Rg total_rg21.09
Total atoms total_atoms2957
Residues n_residues356
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 dmax65.5
Rg (real space) rg_real21.17
Rg uncertainty (real space) rg_real_error0.25
I(0) (real space) i0_real2.7370e+07
I(0) uncertainty (real space) i0_real_error3.1130e+05
Rg (reciprocal space) rg_reciprocal21.20
I(0) (reciprocal space) i0_reciprocal27370000.0000
Solution quality estimate total_estimate0.8999
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary64.5
Skewness Skewness skewness0.150
Kurtosis Kurtosis kurtosis-0.424
Angular range angular_range— – 0.3750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8691000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2f7ze_
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_id2f7zE01
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_id2f7zE02
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)