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- PDB-1bdy: C2 DOMAIN FROM PROTEIN KINASE C DELTA -

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Basic information

Entry
Database: PDB / ID: 1bdy
TitleC2 DOMAIN FROM PROTEIN KINASE C DELTA
ComponentsPROTEIN KINASE C
KeywordsCALCIUM-BINDING / PROTEIN KINASE C / C2 DOMAIN / CALCIUM / DUPLICATION / ATP-BINDING / TRANSFERASE
Function / homology
Function and homology information


DAG and IP3 signaling / CLEC7A (Dectin-1) signaling / HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of glucosylceramide catabolic process / Calmodulin induced events / SHC1 events in ERBB2 signaling / positive regulation of sphingomyelin catabolic process / histone H2AXY142 kinase activity / Role of phospholipids in phagocytosis / regulation of ceramide biosynthetic process ...DAG and IP3 signaling / CLEC7A (Dectin-1) signaling / HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of glucosylceramide catabolic process / Calmodulin induced events / SHC1 events in ERBB2 signaling / positive regulation of sphingomyelin catabolic process / histone H2AXY142 kinase activity / Role of phospholipids in phagocytosis / regulation of ceramide biosynthetic process / Effects of PIP2 hydrolysis / VEGFR2 mediated cell proliferation / TIR domain binding / endolysosome / negative regulation of filopodium assembly / Apoptotic cleavage of cellular proteins / positive regulation of ceramide biosynthetic process / termination of signal transduction / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / RHO GTPases Activate NADPH Oxidases / diacylglycerol-dependent serine/threonine kinase activity / cellular response to hydroperoxide / Interferon gamma signaling / D-aspartate import across plasma membrane / negative regulation of glial cell apoptotic process / collagen metabolic process / negative regulation of actin filament polymerization / histone H3Y41 kinase activity / neutrophil activation / negative regulation of platelet aggregation / regulation of phosphorylation / Neutrophil degranulation / B cell proliferation / immunoglobulin mediated immune response / postsynaptic cytosol / insulin receptor substrate binding / cellular response to angiotensin / response to amino acid / response to glucose / response to mechanical stimulus / cellular response to glucose starvation / negative regulation of insulin receptor signaling pathway / post-translational protein modification / enzyme activator activity / positive regulation of superoxide anion generation / positive regulation of apoptotic signaling pathway / positive regulation of D-glucose import / cell chemotaxis / regulation of actin cytoskeleton organization / : / response to hydrogen peroxide / cellular response to hydrogen peroxide / positive regulation of protein import into nucleus / nuclear matrix / cellular response to insulin stimulus / cellular response to UV / cellular senescence / cell-cell junction / peptidyl-serine phosphorylation / cellular response to oxidative stress / response to oxidative stress / response to ethanol / response to hypoxia / protein kinase activity / positive regulation of MAPK cascade / intracellular signal transduction / defense response to bacterium / positive regulation of apoptotic process / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / mitochondrion / ATP binding / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein kinase C delta type
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsPappa, H. / Murray-Rust, J. / Dekker, L.V. / Parker, P.J. / Mcdonald, N.Q.
CitationJournal: Structure / Year: 1998
Title: Crystal structure of the C2 domain from protein kinase C-delta.
Authors: Pappa, H. / Murray-Rust, J. / Dekker, L.V. / Parker, P.J. / McDonald, N.Q.
History
DepositionMay 11, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN KINASE C
B: PROTEIN KINASE C


Theoretical massNumber of molelcules
Total (without water)28,0282
Polymers28,0282
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.720, 60.690, 120.900
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 PROTEIN KINASE C / PKC


Mass: 14014.211 Da / Num. of mol.: 2 / Fragment: C2-DOMAIN / Mutation: GLY-SER-HIS AT THE N-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P09215, EC: 2.7.1.37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLISED FROM 20% PEG 4000, 0.2M NH4 ACETATE, 0.1M CITRATE, PH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Pappa, H.S., (1998) Acta Cryst., D54, 693.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
25 mg/mlprotein1drop
1PEG40001drop
3PEG40001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 13223 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.071
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 36783 / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -10.1 %RANDOM
Rwork0.1976 ---
obs0.1976 13223 96 %-
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.206 Å20 Å20 Å2
2---0.115 Å20 Å2
3---1.868 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 0 74 2000
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.595
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.317
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.951.5
X-RAY DIFFRACTIONx_mcangle_it3.382
X-RAY DIFFRACTIONx_scbond_it3.32
X-RAY DIFFRACTIONx_scangle_it5.092.5
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.3549 -
Rwork0.2832 413
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2473
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.317

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