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- PDB-9geb: Trp-cage fortified Tc5b-Exenatide chimera (Ex-4-Tc5bQR) at 288K -

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Basic information

Entry
Database: PDB / ID: 9geb
TitleTrp-cage fortified Tc5b-Exenatide chimera (Ex-4-Tc5bQR) at 288K
ComponentsTrp-cage fortified Tc5b-Exenatide chimera (Ex-4-Tc5bQR)
KeywordsDE NOVO PROTEIN / Exenatide / GLP-1R ligand / Trp-Cage DE NOVO PROTEIN / Miniprotein / Disulfide bond
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 Communitys Seventh Framework ProgrammeRRF-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
DepositionAug 7, 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: Trp-cage fortified Tc5b-Exenatide chimera (Ex-4-Tc5bQR)


Theoretical massNumber of molelcules
Total (without water)2,7851
Polymers2,7851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Trp-cage fortified Tc5b-Exenatide chimera (Ex-4-Tc5bQR)


Mass: 2785.094 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)
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: 0.65 mM non-labeled polypeptide, 1 % non-labeled sodium azide, 1 % non-labeled DSS, 90% H2O/10% D2O
Label: 1H / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.65 mMpolypeptidenon-labeled1
1 %sodium azidenon-labeled1
1 %DSSnon-labeled1
Sample conditionsIonic strength: n.d. Not defined / Label: 1 / pH: 7.14 / Pressure: 1 atm / Temperature: 288 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 Assign2.4.1.CCPNrefinement
ARIA2alpha2.3.1.CCPNstructure calculation
CcpNmr Analysis Assign2.4.1.CCPNchemical shift assignment
CcpNmr Analysis Assign2.4.1.CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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