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- PDB-6gdz: exendin-4 based dual GLP-1/glucagon receptor agonist -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6gdz
Titleexendin-4 based dual GLP-1/glucagon receptor agonist
ComponentsExendin-4
KeywordsHORMONE
Function / homology
Function and homology information


hormone activity / regulation of blood pressure / toxin activity / extracellular region
Similarity search - Function
Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones
Similarity search - Domain/homology
Chem-EVT / Exendin-4
Similarity search - Component
Biological speciesHeloderma suspectum (Gila monster)
MethodSOLUTION NMR / molecular dynamics
AuthorsEvers, A. / Kurz, M.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Dual Glucagon-like Peptide 1 (GLP-1)/Glucagon Receptor Agonists Specifically Optimized for Multidose Formulations.
Authors: Evers, A. / Bossart, M. / Pfeiffer-Marek, S. / Elvert, R. / Schreuder, H. / Kurz, M. / Stengelin, S. / Lorenz, M. / Herling, A. / Konkar, A. / Lukasczyk, U. / Pfenninger, A. / Lorenz, K. / ...Authors: Evers, A. / Bossart, M. / Pfeiffer-Marek, S. / Elvert, R. / Schreuder, H. / Kurz, M. / Stengelin, S. / Lorenz, M. / Herling, A. / Konkar, A. / Lukasczyk, U. / Pfenninger, A. / Lorenz, K. / Haack, T. / Kadereit, D. / Wagner, M.
History
DepositionApr 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exendin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6572
Polymers4,1431
Non-polymers5151
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area110 Å2
ΔGint0 kcal/mol
Surface area3920 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Exendin-4


Mass: 4142.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Heloderma suspectum (Gila monster) / References: UniProt: P26349
#2: Chemical ChemComp-EVT / (2~{S})-2-[[(4~{S})-4-(hexadecanoylamino)-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]pentanedioic acid


Mass: 514.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H46N2O8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic22D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 5 mg/mL Peptide 5, trifluoroethanol/water / Label: Model 1 / Solvent system: trifluoroethanol/water
SampleConc.: 5 mg/mL / Component: Peptide 5 / Isotopic labeling: none
Sample conditionsIonic strength: 35mM sodium phosphate M / Ionic strength err: 0.2 / Label: conditions_1 / pH: 5.0 / PH err: 0.05 / Pressure: 1 Pa / Pressure err: 0.01 / Temperature: 310 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker 1Bruker17001AVANCE I
Bruker 2Bruker25002AVANCE II

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinchemical shift assignment
SYBYL2.1.1Triposstructure calculation
CARARelease 1.8.4.2Keller and Wuthrichchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 10

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