- PDB-3agl: Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1039 -
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Basic information
Entry
Database: PDB / ID: 3agl
Title
Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1039
Components
cAMP-dependent protein kinase catalytic subunit alpha
Keywords
TRANSFERASE/TRANSFERASE INHIBITOR / PKA / protein kinase A / bisubstrate inhibitor / ARC-1039 / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information
PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / Mitochondrial protein degradation / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / Factors involved in megakaryocyte development and platelet production / cellular response to heat / manganese ion binding / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / mitochondrial matrix / protein domain specific binding / protein phosphorylation Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 80 mM Mes-BisTris, 75 mM LiCl, 1.5 mM octanoyl-N-methylglucamide; mixed 2:1 with and equilibrated against 40%(v/v) MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution: 2.1→52.32 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.216 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
2459
5.1 %
RANDOM
Rwork
0.198
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-
-
obs
0.2
46179
99.95 %
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all
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48661
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 23.3 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.03 Å2
0 Å2
0 Å2
2-
-
-0.15 Å2
0 Å2
3-
-
-
0.17 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→52.32 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5607
0
126
235
5968
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
5883
X-RAY DIFFRACTION
r_angle_refined_deg
1.258
1.977
7939
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.361
5
676
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.061
24.126
286
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.529
15.043
1040
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.737
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.091
0.2
826
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
4456
X-RAY DIFFRACTION
r_mcbond_it
0.697
1.5
3390
X-RAY DIFFRACTION
r_mcangle_it
1.323
2
5478
X-RAY DIFFRACTION
r_scbond_it
2.02
3
2493
X-RAY DIFFRACTION
r_scangle_it
3.315
4.5
2461
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.274
185
-
Rwork
0.222
3351
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obs
-
-
99.97 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.722
0.0636
0.1115
2.2964
-0.9219
1.1376
-0.0228
0.0648
0.0415
-0.0506
-0.0318
-0.1704
-0.0971
0.0843
0.0547
0.0221
-0.0036
0.0111
0.0727
0.0062
0.0281
-11.043
0.172
7.872
2
1.1787
-0.0045
0.2126
2.4223
-0.4926
0.776
-0.0114
0.0987
0.1863
-0.0641
-0.0147
-0.0565
-0.0987
0.0097
0.0262
0.0209
-0.0018
0.003
0.0524
0.015
0.0313
-11.259
50.033
-25.233
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-10 - 9999
2
X-RAY DIFFRACTION
2
A - B
-10 - 9999
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