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- PDB-7mll: Solution structure of Exenatide (exendin-4) in 30-vol% trifluoroe... -

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Basic information

Entry
Database: PDB / ID: 7mll
TitleSolution structure of Exenatide (exendin-4) in 30-vol% trifluoroethanol using CS-Rosetta
ComponentsExendin-4
KeywordsPROTEIN BINDING / anti-diabetic drug / signaling receptor binding
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 / molecular dynamics
AuthorsMishra, S.H. / Bhavaraju, S.
CitationJournal: J Pharm Biomed Anal / Year: 2021
Title: Facilitated structure verification of the biopharmaceutical peptide exenatide by 2D heteronuclear NMR maps.
Authors: Mishra, S.H. / Bhavaraju, S. / Schmidt, D.R. / Carrick, K.L.
History
DepositionApr 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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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)4,1901
Polymers4,1901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120 Å2
ΔGint1 kcal/mol
Surface area3070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 3000structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Exendin-4


Mass: 4189.596 Da / Num. of mol.: 1 / Fragment: UNP Residue 48-86 / Source method: obtained synthetically / Source: (synth.) Heloderma suspectum (Gila monster) / References: UniProt: P26349
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-13C HSQC TOCSY
141isotropic12D 1H-15N HSQC TOCSY
151isotropic12D 1H-13C HMBC (carbonyl selective)
161isotropic11D 13C APT

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Sample preparation

DetailsType: solution
Contents: 13 mM 'NA-' Exenatide (exendin-4), 20 mM 'NA-' sodium phosphate, 30 % v/v [U-99% 2H] TFE, 10 % v/v [U-99% 2H] D2O, 0.01 mg/mL 'NA-' DSS, 60 % H2O/30%Trifluoroethanol/10 % D2O
Label: Exenatide_30mg / Solvent system: 60 % H2O/30%Trifluoroethanol/10 % D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
13 mMExenatide (exendin-4)'NA-'1
20 mMsodium phosphate'NA-'1
30 % v/vTFE[U-99% 2H]1
10 % v/vD2O[U-99% 2H]1
0.01 mg/mLDSS'NA-'1
Sample conditionsIonic strength: 20 mM / Label: Exenatide_30mg / pH: 5.35 / Pressure: 1 atm / Temperature: 315 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Bax Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples" Oliver F. Lange; Paolo Rossi; Nikolaos G. Sgourakis; Yifan Song; Hsiau-Wei Lee; James M. Aramini; Asli Ertekin; Rong Xiao; Thomas B. Acton; Gaetano T. Montelione; David Baker; Proceedings of the National Academy of Sciences 109(27) 10873-10878 (2012) doi: 10.1073/pnas.1203013109 "De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds," Yang Shen; Philip N. Bryan; Yanan He; John Orban; David Baker; Ad Bax; Protein Science 19, 349-356 (2010) doi: 10.1002/pro.303 "De novo protein structure generation from incomplete chemical shift assignments," Yang Shen; Robert Vernon; David Baker; Ad Bax; J. Biomol. NMR 43, 63-78 (2009) doi: 10.1007/s10858-008-9288-5 "Consistent blind protein structure generation from NMR chemical shift data," Yang Shen; Oliver Lange; Frank Delaglio; Paolo Rossi; James M. Aramini; Gaohua Liu; Alexander Eletsky; Yibing Wu; Kiran K. Singarapu; Alexander Lemak; Alexandr Ignatchenko; Cheryl H. Arrowsmith; Thomas Szyperski; Gaetano T. Montelione; David Baker; Ad Bax; Proceedings of the National Academy of Sciences 105(12) 4685-4690 (2008) doi: 10.1073/pnas.0800256105structure calculation
RosettaFiras Khatib 1, Seth Cooper, Michael D Tyka, Kefan Xu, Ilya Makedon, Zoran Popovic, David Baker, Foldit Players - Algorithm discovery by protein folding game players. Jack B. Maguire Hugh K. Haddox Devin Strickland Samer F. Halabiya Brian Coventry Jermel R. Griffin Surya V. S. R. K Pulavarti Matthew Cummins David F Thieker Eric Klavins Thomas Szyperski Frank DiMaio David Baker Brian Kuhlman - Perturbing the energy landscape for improved packing during computational protein designrefinement
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 5

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