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- PDB-2m3n: Peptide leucine arginine -

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Basic information

Entry
Database: PDB / ID: 2m3n
TitlePeptide leucine arginine
ComponentsPeptide leucine arginine
KeywordsHydrolase inhibitor / bowman birk inhibitor
Function / homology
Function and homology information


mast cell degranulation / defense response to fungus / defense response / killing of cells of another organism / defense response to Gram-positive bacterium / inflammatory response / extracellular region
Similarity search - Function
Frog antimicrobial peptide, ranacyclin-type, Ranidae / Frog antimicrobial peptide / Frog antimicrobial peptide, propeptide / Frog skin active peptide family signal and propeptide
Similarity search - Domain/homology
Peptide leucine arginine
Similarity search - Component
Biological speciesRana pipiens (northern leopard frog)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsPolte, T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Therapeutic potential of the Peptide leucine arginine as a new nonplant bowman-birk-like serine protease inhibitor.
Authors: Rothemund, S. / Sonnichsen, F.D. / Polte, T.
History
DepositionJan 23, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide leucine arginine


Theoretical massNumber of molelcules
Total (without water)2,1421
Polymers2,1421
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 Peptide leucine arginine / pLR


Mass: 2141.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rana pipiens (northern leopard frog) / References: UniProt: Q90WP7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
2312D 1H-1H NOESY
3412D 1H-1H NOESY
1512D 1H-1H TOCSY
2612D 1H-1H TOCSY
3712D 1H-1H TOCSY
1822D DQF-COSY
1922D 1H-1H NOESY
11022D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM peptide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM peptide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMpeptide1
1 mMpeptide2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
103.5ambient 298 K
2ambient 293 K
3ambient 310 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
NMRView8.0.3Johnson, One Moon Scientificchemical shift assignment
NMRView8.0.3Johnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: WITH EXPLICIT WATER, WATER REFINEMENT WITH RECOORD SCRIPTS
NMR constraintsProtein phi angle constraints total count: 10 / Protein psi angle constraints total count: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 2.4 ° / Maximum upper distance constraint violation: 0.273 Å / Torsion angle constraint violation method: 1D, TALOS+
NMR ensemble rmsDistance rms dev: 0.0276 Å / Distance rms dev error: 0.0056 Å

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