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- PDB-2bey: Solution Structure of a Novel C2 Symmetrical Bifunctional Bicycli... -

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Basic information

Entry
Database: PDB / ID: 2bey
TitleSolution Structure of a Novel C2 Symmetrical Bifunctional Bicyclic Inhibitor Based on SFTI-1
ComponentsBIKK
KeywordsINHIBITOR / BIKK / C2 SYMMETRICAL BIFUNCTIONAL BICYCLIC TRYPSIN INHIBITOR / SYMMETRY / SFTI1
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsJaulent, A.M. / Brauer, A.B.E. / Matthews, S.J. / Leatherbarrow, R.J.
Citation
Journal: J.Biomol.NMR / Year: 2005
Title: Solution Structure of a Novel C2-Symmetrical Bifunctional Bicyclic Inhibitor Based on Sfti-1
Authors: Jaulent, A.M. / Brauer, A.B.E. / Matthews, S.J. / Leatherbarrow, R.J.
#1: Journal: Protein Eng.Des.Sel. / Year: 2004
Title: Design, Synthesis and Analysis of Novel Bicyclic and Bifunctional Protease Inhibitors
Authors: Jaulent, A.M. / Leatherbarrow, R.J.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: High-Resolution Structure of a Potent, Cyclic Proteinase Inhibitor from Sunflower Seeds
Authors: Luckett, S. / Garcia, R.S. / Barker, J.J. / Konarev, A.V. / Shewry, P.R. / Clarke, A.R. / Brady, R.L.
History
DepositionDec 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Derived calculations / Other ...Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIKK


Theoretical massNumber of molelcules
Total (without water)1,7001
Polymers1,7001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide BIKK


Mass: 1700.114 Da / Num. of mol.: 1 / Fragment: DUPLICATED AND FUSED REACTIVE SITE LOOP OF SFTI-1 / Source method: obtained synthetically
Details: THE PEPTIDE IS BACKBONE CYCLIZED (CYS1-ILE16) AND HAS AN INTRAMOLECULAR DISULFIDE BOND (CYS1-CYS9)
Source: (synth.) SYNTHETIC CONSTRUCT (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H-NMR. NO HYDROGEN BOND RESTRAINTS WERE USED IN THE STRUCTURE CALCULATIONS.

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Sample preparation

Sample conditionspH: 3.8 / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TINKER/DISTGEOMJ.W.PONDERrefinement
TINKER/ISTGEOMstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers submitted total number: 20

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