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- PDB-1d0r: SOLUTION STRUCTURE OF GLUCAGON-LIKE PEPTIDE-1-(7-36)-AMIDE IN TRI... -

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Basic information

Entry
Database: PDB / ID: 1d0r
TitleSOLUTION STRUCTURE OF GLUCAGON-LIKE PEPTIDE-1-(7-36)-AMIDE IN TRIFLUOROETHANOL/WATER
ComponentsGLUCAGON-LIKE PEPTIDE-1-(7-36)-AMIDE
KeywordsHORMONE/GROWTH FACTOR / SYNTHETIC HORMONE / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


glucagon receptor binding / protein kinase A signaling / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / regulation of insulin secretion / cellular response to glucagon stimulus ...glucagon receptor binding / protein kinase A signaling / negative regulation of execution phase of apoptosis / feeding behavior / positive regulation of calcium ion import / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of gluconeogenesis / regulation of insulin secretion / cellular response to glucagon stimulus / response to activity / gluconeogenesis / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon signaling in metabolic regulation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / glucose homeostasis / secretory granule lumen / G alpha (s) signalling events / G alpha (q) signalling events / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Glucagon / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsChang, X. / Keller, D. / Bjorn, S. / Led, J.J.
Citation
Journal: MAGN.RESON.CHEM. / Year: 2001
Title: Structure and Folding of Glucagon-like Peptide-1-(7-36)-amide in Trifluoroethanol Studied by NMR
Authors: Chang, X. / Keller, D. / Bjorn, S. / Led, J.J.
#1: Journal: FEBS Lett. / Year: 2002
Title: NMR studies of the aggregation of glucagon-like peptide-1: formation of a symmetric helical dimer
Authors: Chang, X. / Keller, D. / O'Donoghue, S.I. / Led, J.J.
History
DepositionSep 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 25, 2016Group: Source and taxonomy
Revision 1.4Jan 31, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name
Revision 1.5Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCAGON-LIKE PEPTIDE-1-(7-36)-AMIDE


Theoretical massNumber of molelcules
Total (without water)3,3031
Polymers3,3031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #10lowest energy

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Components

#1: Protein/peptide GLUCAGON-LIKE PEPTIDE-1-(7-36)-AMIDE


Mass: 3302.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RECOMBINANT FORM / Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01275

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
1422D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

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Sample preparation

Details
Solution-IDContents
11.4MM GLUCAGON-LIKE PEPTIDE 1-(7-36)-AMIDE
21.4MM GLUCAGON-LIKE PEPTIDE 1-(7-36)-AMIDE
Sample conditionspH: 2.5 / Pressure: AMBIENT / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMBrukerAM5001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 280 NOE-DERIVED DISTANCE CONSTRAINTS, AND 24 DISTANCE RESTRAINTS FROM HYDROGEN BONDS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20
NMR ensemble rmsAtom type: all backbone atoms / Bond angle rms dev: 3.3 ° / Chain range begin: A / Chain range end: A
Coord average rmsd method: THE AVERAGE OF THE RMSD TO THE MEAN OF THE 20 NMR CONFORMERS AS DESCRIBED IN REFERENCE JRNL IS 2.92 ANGSTROMS FOR THE N, C AND CA BACKBONE ATOMS
Covalent bond rms dev: 0.0144 Å / Improper torsion angle rms dev: 0.33 ° / Residue range begin: 1 / Residue range end: 30

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