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- PDB-2p5j: sPLA2 inhibitor pip 17 -

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Basic information

Entry
Database: PDB / ID: 2p5j
TitlesPLA2 inhibitor pip 17
Componentspip17
KeywordsHYDROLASE inhibitor / sPLA2 / inhibitor / arthritis
MethodSOLUTION NMR / torsion angle dynamics
AuthorsThwin, M.M. / Satyanarayanajois, D.S. / Nagarajarao, L.M. / Sato, K. / Gopalakrishnakone, P.P. / Arjunan, P.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Novel Peptide Inhibitors of Human Secretory Phospholipase A2 with Antiinflammatory Activity: Solution Structure and Molecular Modeling.
Authors: Thwin, M.M. / Satyanarayanajois, S.D. / Nagarajarao, L.M. / Sato, K. / Arjunan, P. / Ramapatna, S.L. / Kumar, P.V. / Gopalakrishnakone, P.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pip17


Theoretical massNumber of molelcules
Total (without water)2,0151
Polymers2,0151
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 least restraint violations
Representative

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Components

#1: Protein/peptide pip17


Mass: 2015.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: DMSO / Solvent system: DMSO
Sample conditionsPressure: 1 atm / Temperature units: K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1GUNTERT, P. ET AL.refinement
CYANA2.1GUNTERT, P. ET AL.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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