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- PDB-2c1a: Structure of cAMP-dependent protein kinase complexed with Isoquin... -

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Basic information

Entry
Database: PDB / ID: 2c1a
TitleStructure of cAMP-dependent protein kinase complexed with Isoquinoline-5-sulfonic acid (2-(2-(4-chlorobenzyloxy)ethylamino) ethyl)amide
Components
  • CAMP-DEPENDENT PROTEIN KINASE
  • CAMP-DEPENDENT PROTEIN KINASE INHIBITOR
KeywordsTRANSFERASE/INHIBITOR / COMPLEX (TRANSFERASE-INHIBITOR) / ATP-BINDING / CAMP / PHOSPHORYLATION / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / PROTEIN KINASE INHIBITOR / TRANSFERASE-INHIBITOR complex
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-I5S / 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: 1.95 Å
AuthorsCollins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. ...Collins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. / Berdini, V. / Woodhead, S.J. / Seavers, L.C.A. / Wyatt, P.G. / Workman, P. / McDonald, E.
CitationJournal: Bioorg. Med. Chem. / Year: 2006
Title: Structure-based design of isoquinoline-5-sulfonamide inhibitors of protein kinase B.
Authors: Collins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. / Berdini, V. / Woodhead, S.J. / Davis, D. ...Authors: Collins, I. / Caldwell, J. / Fonseca, T. / Donald, A. / Bavetsias, V. / Hunter, L.J. / Garrett, M.D. / Rowlands, M.G. / Aherne, G.W. / Davies, T.G. / Berdini, V. / Woodhead, S.J. / Davis, D. / Seavers, L.C. / Wyatt, P.G. / Workman, P. / McDonald, E.
History
DepositionSep 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4843
Polymers43,0642
Non-polymers4201
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.364, 75.097, 80.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE CAMP-DEPENDENT PROTEIN KINASE IS A MONOMER ININ THE ABSENCE OF THE REGULATORY SUBUNIT . IN THISENTRY THIS IS ANNOTATED AS A DIMER SINCE THIS ISIN COMPLEX WITH PEPTIDE CHAIN I.

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Components

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


Mass: 40837.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide CAMP-DEPENDENT PROTEIN KINASE INHIBITOR / ALPHA FORM / PKI-ALPHA / CAMP-DEPENDENT PROTEIN KINASE INHIBITOR / MUSCLE/BRAIN ISOFORM


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925
#3: Chemical ChemComp-I5S / ISOQUINOLINE-5-SULFONIC ACID (2-(2-(4-CHLOROBENZYLOXY)ETHYLAMINO)ETHYL)AMIDE


Mass: 419.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22ClN3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.53 Å3/Da / Density % sol: 51.31 %

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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: 1.95→35 Å / Num. obs: 31729 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.2 / % possible all: 88.8

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Processing

SoftwareName: REFMAC / Version: 5.1.29 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YDS

1yds


Resolution: 1.95→35.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.652 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1599 5 %RANDOM
Rwork0.173 ---
obs0.176 30093 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2---0.26 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 28 415 3382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223044
X-RAY DIFFRACTIONr_bond_other_d0.0020.022715
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9574108
X-RAY DIFFRACTIONr_angle_other_deg0.8236328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023327
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02662
X-RAY DIFFRACTIONr_nbd_refined0.2330.2657
X-RAY DIFFRACTIONr_nbd_other0.2410.23224
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21757
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2313
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.81751773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.93362862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.86861271
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4487.51246
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 99
Rwork0.225 1898

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