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- PDB-1tbo: NMR STRUCTURE OF A PROTEIN KINASE C-G PHORBOL-BINDING DOMAIN, 30 ... -

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Entry
Database: PDB / ID: 1tbo
TitleNMR STRUCTURE OF A PROTEIN KINASE C-G PHORBOL-BINDING DOMAIN, 30 STRUCTURES
ComponentsPROTEIN KINASE C, GAMMA TYPE
KeywordsCALCIUM-BINDING PROTEIN / PROTEIN KINASE C / PKC / TRANSFERASE
Function / homology
Function and homology information


Calmodulin induced events / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / calcium,diacylglycerol-dependent serine/threonine kinase activity / regulation of response to food / positive regulation of mismatch repair / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process ...Calmodulin induced events / Disinhibition of SNARE formation / Response to elevated platelet cytosolic Ca2+ / calcium,diacylglycerol-dependent serine/threonine kinase activity / regulation of response to food / positive regulation of mismatch repair / WNT5A-dependent internalization of FZD4 / protein kinase C / chemosensory behavior / negative regulation of proteasomal protein catabolic process / diacylglycerol-dependent serine/threonine kinase activity / innervation / regulation of phagocytosis / presynaptic cytosol / response to morphine / regulation of synaptic vesicle exocytosis / postsynaptic cytosol / response to pain / response to psychosocial stress / Trafficking of GluR2-containing AMPA receptors / calyx of Held / phosphorylation / negative regulation of protein ubiquitination / protein serine/threonine/tyrosine kinase activity / presynaptic modulation of chemical synaptic transmission / synaptic membrane / long-term synaptic potentiation / regulation of circadian rhythm / negative regulation of protein catabolic process / response to toxic substance / cell-cell junction / rhythmic process / presynapse / peptidyl-serine phosphorylation / chemical synaptic transmission / negative regulation of neuron apoptotic process / protein autophosphorylation / postsynaptic density / learning or memory / protein kinase activity / intracellular signal transduction / neuron projection / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / perinuclear region of cytoplasm / zinc ion binding / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein kinase C, alpha/beta/gamma 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. / Protein kinase C conserved region 2 (CalB) / C2 domain ...Protein kinase C, alpha/beta/gamma 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. / Protein kinase C conserved region 2 (CalB) / C2 domain / 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
Protein kinase C gamma type / Protein kinase C gamma type
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodSOLUTION NMR / DG-SA
AuthorsXu, R.X. / Pawelczyk, T. / Xia, T. / Brown, S.C.
Citation
Journal: Biochemistry / Year: 1997
Title: NMR structure of a protein kinase C-gamma phorbol-binding domain and study of protein-lipid micelle interactions.
Authors: Xu, R.X. / Pawelczyk, T. / Xia, T.H. / Brown, S.C.
#1: Journal: 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.
#2: Journal: J.Biochem.(Tokyo) / Year: 1995
Title: Solution Structure of Cysteine-Rich Domain of Protein Kinase C Alpha
Authors: Ichikawa, S. / Hatanaka, H. / Takeuchi, Y. / Ohno, S. / Inagaki, F.
#3: Journal: Nat.Struct.Biol. / Year: 1994
Title: Solution Structure of a Cysteine Rich Domain of Rat Protein Kinase C
Authors: Hommel, U. / Zurini, M. / Luyten, M.
History
DepositionApr 15, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN KINASE C, GAMMA TYPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4903
Polymers9,3601
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 1
Representative

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Components

#1: Protein PROTEIN KINASE C, GAMMA TYPE / RAT BRAIN PKC-G


Mass: 9359.666 Da / Num. of mol.: 1 / Fragment: CYS2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Organ: BRAIN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P05697, UniProt: P63319*PLUS, 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.5 / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameClassification
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: DG-SA / Software ordinal: 1
NMR ensembleConformers calculated total number: 1 / Conformers submitted total number: 30

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