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- PDB-9g0n: Trp-cage fortified Tc5b-Exenatide chimera (Ex4-Tc5bER) at 299K -

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Basic information

Entry
Database: PDB / ID: 9g0n
TitleTrp-cage fortified Tc5b-Exenatide chimera (Ex4-Tc5bER) at 299K
ComponentsExendin-4
KeywordsDE NOVO PROTEIN / Exenatide / GLP-1R ligand / Trp-cage
Function / homologyGlucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / hormone activity / regulation of blood pressure / toxin activity / extracellular region / Exendin-4
Function and homology information
Biological speciesHeloderma suspectum (Gila monster)
MethodSOLUTION NMR / simulated annealing
AuthorsHorvath, D.
Funding support Hungary, European Union, 2items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation Office2018-1.2.1-NKP-2018-00005 Hungary
European CommissionRRF-2.3.1-21-2022-00015European Union
CitationJournal: J.Med.Chem. / Year: 2024
Title: Influence of Trp-Cage on the Function and Stability of GLP-1R Agonist Exenatide Derivatives.
Authors: Horvath, D. / Straner, P. / Taricska, N. / Fazekas, Z. / Menyhard, D.K. / Perczel, A.
History
DepositionJul 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exendin-4


Theoretical massNumber of molelcules
Total (without water)2,7861
Polymers2,7861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Exendin-4


Mass: 2786.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heloderma suspectum (Gila monster) / Production host: Escherichia coli (E. coli) / References: UniProt: P26349
Has protein modificationN

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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

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Sample preparation

DetailsType: solution
Contents: 0.8 mM non-labelled polypeptide, 1 % non-labelled sodium-azide, 1 % non-labelled DSS, 90% H2O/10% D2O
Label: non-labelled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMpolypeptidenon-labelled1
1 %sodium-azidenon-labelled1
1 %DSSnon-labelled1
Sample conditionsIonic strength: n.d. Not defined / Label: 1 / pH: 7 / PH err: 0.2 / Pressure: 1 atm / Temperature: 299 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis Assign2.4.1CCPNrefinement
ARIA2alpha2.3.1Rieping, W.structure calculation
CcpNmr Analysis Assign2.4.1CCPNchemical shift assignment
CcpNmr Analysis Assign2.4.1CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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