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- PDB-2jds: Structure of cAMP-dependent protein kinase complexed with A-443654 -

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Basic information

Entry
Database: PDB / ID: 2jds
TitleStructure of cAMP-dependent protein kinase complexed with A-443654
Components
  • CAMP-DEPENDENT PROTEIN KINASE
  • CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
KeywordsTRANSFERASE / CAMP / KINASE / MYRISTATE / LIPOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / PROTEIN KINASE INHIBITOR / ATP-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Loss of Nlp from mitotic centrosomes ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of cAMP-dependent protein kinase activity / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / Mitochondrial protein degradation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein kinase A regulatory subunit binding / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / regulation of proteasomal protein catabolic process / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / positive regulation of phagocytosis / protein export from nucleus / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / peptidyl-serine phosphorylation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / protein phosphorylation / postsynapse / protein kinase activity / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Chem-L20 / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDavies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / McHardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. ...Davies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / McHardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. / Jhoti, H. / Barford, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A Structural Comparison of Inhibitor Binding to Pkb, Pka and Pka-Pkb Chimera
Authors: Davies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / Mchardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. / Jhoti, H. / Barford, D.
History
DepositionJan 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE
I: CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5413
Polymers43,1442
Non-polymers3971
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.538, 75.061, 80.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CAMP-DEPENDENT PROTEIN KINASE / PROTEIN KINASE A / PKA C-ALPHA


Mass: 40917.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ALPHA-CATALYTIC SUBUNIT / Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase
#2: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA / PKI-ALPHA / CAMP-DEPENDENT PROTEIN KINASE INHIBITOR


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925
#3: Chemical ChemComp-L20 / (2S)-1-(1H-INDOL-3-YL)-3-{[5-(3-METHYL-1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}PROPAN-2-AMINE


Mass: 397.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.46 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→36 Å / Num. obs: 28286 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 95

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Processing

SoftwareName: REFMAC / Version: 5.2.0019C / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YDS

1yds


Resolution: 2→36.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.964 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1512 5.1 %RANDOM
Rwork0.208 ---
obs0.211 28286 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 30 325 3302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223056
X-RAY DIFFRACTIONr_bond_other_d0.0010.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9674129
X-RAY DIFFRACTIONr_angle_other_deg0.87535108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60823.961154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39915.111541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5531518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
X-RAY DIFFRACTIONr_nbd_refined0.2030.2628
X-RAY DIFFRACTIONr_nbd_other0.190.22200
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21470
X-RAY DIFFRACTIONr_nbtor_other0.0840.21550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.05851777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.07762868
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.07561279
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0957.51261
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 127
Rwork0.311 1923

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