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- PDB-1ptr: PROTEIN KINASE C DELTA CYS2 DOMAIN COMPLEXED WITH PHORBOL-13-ACETATE -

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Basic information

Entry
Database: PDB / ID: 1ptr
TitlePROTEIN KINASE C DELTA CYS2 DOMAIN COMPLEXED WITH PHORBOL-13-ACETATE
ComponentsPROTEIN KINASE C DELTA TYPE
KeywordsPHOSPHOTRANSFERASE
Function / homology
Function and homology information


DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Effects of PIP2 hydrolysis / regulation of ceramide biosynthetic process / Interferon gamma signaling ...DAG and IP3 signaling / positive regulation of glucosylceramide catabolic process / VEGFR2 mediated cell proliferation / positive regulation of sphingomyelin catabolic process / Apoptotic cleavage of cellular proteins / SHC1 events in ERBB2 signaling / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / Effects of PIP2 hydrolysis / regulation of ceramide biosynthetic process / Interferon gamma signaling / HuR (ELAVL1) binds and stabilizes mRNA / Calmodulin induced events / TIR domain binding / endolysosome / positive regulation of ceramide biosynthetic process / Role of phospholipids in phagocytosis / negative regulation of peptidyl-tyrosine phosphorylation / termination of signal transduction / negative regulation of filopodium assembly / protein kinase C / cellular response to hydroperoxide / D-aspartate import across plasma membrane / CLEC7A (Dectin-1) signaling / diacylglycerol-dependent serine/threonine kinase activity / negative regulation of glial cell apoptotic process / RHO GTPases Activate NADPH Oxidases / negative regulation of actin filament polymerization / collagen metabolic process / neutrophil activation / negative regulation of platelet aggregation / regulation of phosphorylation / cellular response to angiotensin / postsynaptic cytosol / B cell proliferation / insulin receptor substrate binding / immunoglobulin mediated immune response / : / negative regulation of insulin receptor signaling pathway / enzyme activator activity / post-translational protein modification / Neutrophil degranulation / cell chemotaxis / positive regulation of superoxide anion generation / positive regulation of D-glucose import / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of apoptotic signaling pathway / cellular response to hydrogen peroxide / nuclear matrix / positive regulation of protein import into nucleus / cellular response to UV / cellular senescence / cell-cell junction / cellular response to oxidative stress / peptidyl-serine phosphorylation / response to oxidative stress / positive regulation of MAPK cascade / intracellular signal transduction / defense response to bacterium / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / ATP binding / membrane / nucleus / metal ion binding / 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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 domain) ...Protein kinase C, delta / Protein kinase C delta/epsilon/eta/theta, C2 domain / Protein kinase C, delta/epsilon/eta/theta types / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Phorbol esters/diacylglycerol binding domain (C1 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
13-ACETYLPHORBOL / Protein kinase C delta type
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsZhang, G. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of the cys2 activator-binding domain of protein kinase C delta in complex with phorbol ester.
Authors: Zhang, G. / Kazanietz, M.G. / Blumberg, P.M. / Hurley, J.H.
History
DepositionMay 11, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE C DELTA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3494
Polymers5,8121
Non-polymers5373
Water00
1
A: PROTEIN KINASE C DELTA TYPE
hetero molecules

A: PROTEIN KINASE C DELTA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6988
Polymers11,6242
Non-polymers1,0756
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)32.400, 63.500, 65.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide PROTEIN KINASE C DELTA TYPE


Mass: 5811.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: P28867, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PRB / 13-ACETYLPHORBOL


Mass: 406.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30O7

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: used as seeds
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
255 %ammonium sulfate1drop
30.1 Mphosphate1drop
41 mMDTT1drop
525 %isopropanol1reservoir
60.2 Mammonium acetate1reservoir
70.1 Msodium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 5, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 3215 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 3215
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms387 0 31 0 418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
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_deg3.2
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_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.013

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