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- PDB-5h1i: NMR structure of TIBA, a chimera of SFTI -

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Basic information

Entry
Database: PDB / ID: 5h1i
TitleNMR structure of TIBA, a chimera of SFTI
ComponentsBradykinin-trypsin inhibitor secondary loop chimera
KeywordsDE NOVO PROTEIN / TIBA / chimera / sunflower trypsin inhibitor / cyclic peptide
Biological speciesHelianthus annuus (common sunflower)
MethodSOLUTION NMR / simulated annealing
AuthorsXiao, T. / Tam, J.P.
CitationJournal: J. Med. Chem. / Year: 2017
Title: An Orally Active Bradykinin B1 Receptor Antagonist Engineered as a Bifunctional Chimera of Sunflower Trypsin Inhibitor.
Authors: Qiu, Y. / Taichi, M. / Wei, N. / Yang, H. / Luo, K.Q. / Tam, J.P.
History
DepositionOct 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Oct 23, 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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Bradykinin-trypsin inhibitor secondary loop chimera


Theoretical massNumber of molelcules
Total (without water)1,9441
Polymers1,9441
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 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Bradykinin-trypsin inhibitor secondary loop chimera


Mass: 1944.387 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: cyclic peptide of DALK(BA) (RESIDUES 1-10) and TI loop SFTI (RESIDUES 11-18)
Source: (synth.) Helianthus annuus (common sunflower)
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-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.3 mM NA TIBA, 0.01 % NA TFA, 55.56 M NA H2O, 1 mM NA sodium chloride, 95% H2O/5% D2O
Label: 1H_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMTIBANA1
0.01 %TFANA1
55.56 MH2ONA1
1 mMsodium chlorideNA1
Sample conditionsIonic strength: 1 mM / Label: conditions_1 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CNSrefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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