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- PDB-2jdv: Structure of PKA-PKB chimera complexed with A-443654 -

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Basic information

Entry
Database: PDB / ID: 2jdv
TitleStructure of PKA-PKB chimera 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 / Factors involved in megakaryocyte development and platelet production ...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 / Factors involved in megakaryocyte development and platelet production / 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 / RET signaling / AURKA Activation by TPX2 / 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 / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / regulation of osteoblast differentiation / cellular response to cold / Mitochondrial protein degradation / sperm capacitation / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / 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 / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / protein phosphorylation / protein kinase activity / postsynapse / 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 / cytoplasm / cytosol
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: 2.08 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 / Item: _pdbx_entry_details.has_protein_modification

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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)43,4553
Polymers43,0572
Non-polymers3971
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.809, 74.788, 80.363
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: 40830.617 Da / Num. of mol.: 1 / Mutation: YES
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.: 303 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 104 TO THR ENGINEERED RESIDUE IN CHAIN A, VAL 123 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, VAL 104 TO THR ENGINEERED RESIDUE IN CHAIN A, VAL 123 TO ALA ENGINEERED RESIDUE IN CHAIN A, LEU 173 TO MET ENGINEERED RESIDUE IN CHAIN A, GLN 181 TO LYS
Has protein modificationY
Sequence details4 RESIDUES OF THE WILD-TYPE PKA SEQUENCE HAVE BEEN MUTATED TO THE CORRESPONDING RESIDUES IN PKB

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.16 %

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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: 2.08→35 Å / Num. obs: 24115 / % possible obs: 94 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 2.08→35 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.1 / % possible all: 87

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Processing

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

1yds


Resolution: 2.08→35.4 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.369 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1273 5 %RANDOM
Rwork0.206 ---
obs0.21 24115 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.78 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.08→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 30 303 3268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223044
X-RAY DIFFRACTIONr_bond_other_d0.0010.022134
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9664109
X-RAY DIFFRACTIONr_angle_other_deg0.95335164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735.084356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67623.882152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02715.092542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7181518
X-RAY DIFFRACTIONr_chiral_restr0.0930.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_nbd_refined0.2010.2598
X-RAY DIFFRACTIONr_nbd_other0.1930.22226
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21457
X-RAY DIFFRACTIONr_nbtor_other0.0860.21500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3550.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.08651772
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.10962858
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.11361272
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1327.51251
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: 2.08→2.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 93
Rwork0.259 1601

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