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- PDB-2d9z: Solution structure of the PH domain of Protein kinase C, nu type ... -

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Basic information

Entry
Database: PDB / ID: 2d9z
TitleSolution structure of the PH domain of Protein kinase C, nu type from human
ComponentsProtein kinase C, nu type
KeywordsSIGNALING PROTEIN / PH domain / Protein kinase C nu type / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / : / kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / intracellular signal transduction / protein phosphorylation / protein serine kinase activity ...protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / : / kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase C mu-related / Diacylglycerol/phorbol-ester binding / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C1-like domain superfamily / PH-domain like ...Protein kinase C mu-related / Diacylglycerol/phorbol-ester binding / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C1-like domain superfamily / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / 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 / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PH domain of Protein kinase C, nu type from human
Authors: Li, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionDec 13, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase C, nu type


Theoretical massNumber of molelcules
Total (without water)14,3371
Polymers14,3371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein kinase C, nu type / nPKC-nu / Protein kinase EPK2


Mass: 14336.982 Da / Num. of mol.: 1 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PRKCN, EPK2 / Plasmid: P050711-24
References: UniProt: O94806, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.42mM PH domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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