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- PDB-1kx6: NMR solution structure of Glucagon in a lipid-water interphase -

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Basic information

Entry
Database: PDB / ID: 1kx6
TitleNMR solution structure of Glucagon in a lipid-water interphase
ComponentsGlucagon
KeywordsHORMONE/GROWTH FACTOR / hormone / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Glucagon signaling in metabolic regulation / Synthesis, secretion, and deacylation of Ghrelin / glucagon receptor binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / : / lactate biosynthetic process / negative regulation of execution phase of apoptosis / Glucagon-type ligand receptors / G alpha (s) signalling events / G alpha (q) signalling events ...Glucagon signaling in metabolic regulation / Synthesis, secretion, and deacylation of Ghrelin / glucagon receptor binding / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / : / lactate biosynthetic process / negative regulation of execution phase of apoptosis / Glucagon-type ligand receptors / G alpha (s) signalling events / G alpha (q) signalling events / lipid biosynthetic process / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of insulin secretion / positive regulation of protein kinase activity / positive regulation of gluconeogenesis / protein kinase A signaling / response to activity / positive regulation of peptidyl-threonine phosphorylation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / positive regulation of protein binding / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / positive regulation of ERK1 and ERK2 cascade / negative regulation of apoptotic process / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBraun, W. / Wider, G. / Lee, K.H. / Wuthrich, K.
CitationJournal: J.Mol.Biol. / Year: 1983
Title: Conformation of glucagon in a lipid-water interphase by 1H nuclear magnetic resonance.
Authors: Braun, W. / Wider, G. / Lee, K.H. / Wuthrich, K.
History
DepositionJan 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Glucagon


Theoretical massNumber of molelcules
Total (without water)3,4871
Polymers3,4871
Non-polymers00
Water0
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
RepresentativeModel #1minimal target function

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Components

#1: Protein/peptide Glucagon /


Mass: 3486.781 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This protein was chemically synthesized. It is naturally found in Bos taurus (Bovine).
References: UniProt: P01272

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
115mM glucagon; 0.7M [2H38]dodecylphosphocoline; 50mM phosphate buffer100% H2O
215mM glucagon; 0.7M [2H38]dodecylphosphocoline; 50mM phosphate buffer100% D2O
Sample conditionsIonic strength: 50 mM phosphate Na / pH: 6.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker WM / Manufacturer: Bruker / Model: WM / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimal target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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