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- PDB-2m2q: Solution structure of MCh-1: A novel inhibitor cystine knot pepti... -

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Basic information

Entry
Database: PDB / ID: 2m2q
TitleSolution structure of MCh-1: A novel inhibitor cystine knot peptide from Momordica charantia
ComponentsInhibitor cystine knot peptide MCh-1
KeywordsUNKNOWN FUNCTION / cystine knot / disulfide-rich peptides / MCh-1 / oxidative refolding / selective reduction
Function / homologyInhibitor cystine knot peptide MCh-1
Function and homology information
Biological speciesMomordica charantia (bitter melon)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHe, W. / Chan, L. / Clark, R.J. / Tang, J. / Zeng, G. / Franco, O.L. / Cantacessi, C. / Craik, D.J. / Daly, N.L. / Tan, N.
CitationJournal: Plos One / Year: 2013
Title: Novel Inhibitor Cystine Knot Peptides from Momordica charantia.
Authors: He, W.J. / Chan, L.Y. / Clark, R.J. / Tang, J. / Zeng, G.Z. / Franco, O.L. / Cantacessi, C. / Craik, D.J. / Daly, N.L. / Tan, N.H.
History
DepositionJan 1, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Nov 6, 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: Inhibitor cystine knot peptide MCh-1


Theoretical massNumber of molelcules
Total (without water)3,0311
Polymers3,0311
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Inhibitor cystine knot peptide MCh-1


Mass: 3030.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: V5IRT8*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of MCh-1 using NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 3 mM MCh, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 3 mM / Component: MCh-1-1
Sample conditionspH: 5 / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 417 / NOE intraresidue total count: 81 / NOE long range total count: 121 / NOE medium range total count: 61 / NOE sequential total count: 154
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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