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- PDB-6img: Solution Structure of Bicyclic Peptide pb-13 -

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Entry
Database: PDB / ID: 6img
TitleSolution Structure of Bicyclic Peptide pb-13
Components(ACE)-GLY-CYS-PRO-CYS-ILE-TRP-PRO-GLU-LEU-CYS-PRO-TRP-ILE-ARG-SER-CYS-(NH2)
KeywordsDE NOVO PROTEIN / bicyclic peptide / cystine bridge / proline rich
Biological speciesEnterobacteria phage M13 (virus)
MethodSOLUTION NMR / molecular dynamics
AuthorsYao, H. / Lin, P. / Zha, J. / Zha, M. / Zhao, Y. / Wu, C.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Chembiochem / Year: 2019
Title: Ordered and Isomerically Stable Bicyclic Peptide Scaffolds Constrained through Cystine Bridges and Proline Turns.
Authors: Lin, P. / Yao, H. / Zha, J. / Zhao, Y. / Wu, C.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: (ACE)-GLY-CYS-PRO-CYS-ILE-TRP-PRO-GLU-LEU-CYS-PRO-TRP-ILE-ARG-SER-CYS-(NH2)


Theoretical massNumber of molelcules
Total (without water)1,8881
Polymers1,8881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area230 Å2
ΔGint1 kcal/mol
Surface area1660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide (ACE)-GLY-CYS-PRO-CYS-ILE-TRP-PRO-GLU-LEU-CYS-PRO-TRP-ILE-ARG-SER-CYS-(NH2)


Mass: 1888.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage M13 (virus)
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-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H NOESY
251isotropic12D 1H-13C HSQC
261isotropic12D 1H-1H TOCSY
271isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 4.3 mM pb-13, acetonitrile/water
Details: The peptide was dissolved in a mixture of 90% perdeuterated acetonitrile and 10% H2O (pH=1) or D2O (pD=1).
Label: NA_pb13 / Solvent system: acetonitrile/water
SampleConc.: 4.3 mM / Component: pb-13 / Isotopic labeling: natural abundance
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1The peptide was dissolved in a mixture of 90% perdeuterated acetonitrile and 10% H2O (pH=1).0 Not definedACN-H2O11 atm278 K
2The peptide was dissolved in a mixture of 90% perdeuterated acetonitrile and 10% D2O (pD=1).0 Not definedACN-D2O1.0 pD1 atm278 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz / Details: TCI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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