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- PDB-1i6y: NMR ENSEMBLE OF ION-SELECTIVE LIGAND A1 FOR PLATELET INTEGRIN ALP... -

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Basic information

Entry
Database: PDB / ID: 1i6y
TitleNMR ENSEMBLE OF ION-SELECTIVE LIGAND A1 FOR PLATELET INTEGRIN ALPHAIIB-BETA3
ComponentsION-SELECTIVE LIGAND A1
KeywordsCELL ADHESION / integrin / RGD
MethodSOLUTION NMR / restrained molecular dynamics, chemical shift refinement.
AuthorsSmith, J.W. / Le Calvez, H. / Parra-Gessert, L. / Preece, N.E. / Jia, X. / Assa-Munt, N.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Selection and structure of ion-selective ligands for platelet integrin alpha IIb(beta) 3.
Authors: Smith, J.W. / Le Calvez, H. / Parra-Gessert, L. / Preece, N.E. / Jia, X. / Assa-Munt, N.
History
DepositionMar 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ION-SELECTIVE LIGAND A1


Theoretical massNumber of molelcules
Total (without water)1,3251
Polymers1,3251
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)15 / 200structures with the lowest energy
Representative

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Components

#1: Protein/peptide ION-SELECTIVE LIGAND A1


Mass: 1324.555 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized: Commercial solid phase with cyclization via selective disulphide oxidation.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY & DQF-COSY
222
333
444
NMR detailsText: These structures were determined using standard 2D homonuclear techniques (circa 2000).

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Sample preparation

DetailsContents: 3mg/ml A1 / Solvent system: 20mM phosphate buffer; 90% H2O, 10% D2O
Sample conditionsIonic strength: 3mg/ml / pH: 6.5 / Pressure: 1 atm / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian Inc.collection
Felix2000Hare, D.; Biosym; MSIprocessing
X-PLOR3.8.5.1Brunger, A. & Nilges, M.structure solution
X-PLOR3.8.5.1 (Chem.Shift.Module)Kuszweski, J. & Clore, G.M.refinement
RefinementMethod: restrained molecular dynamics, chemical shift refinement.
Software ordinal: 1
Details: Ensemble A1 is based on a total of 117 NOE-derived distance constraints, 10 dihedral angle restraints, 1 covalent -SS- bonds and 1 VRGD, i,i+3 hydrogen bonds respectively. Refinements ...Details: Ensemble A1 is based on a total of 117 NOE-derived distance constraints, 10 dihedral angle restraints, 1 covalent -SS- bonds and 1 VRGD, i,i+3 hydrogen bonds respectively. Refinements incorporated alpha proton and alpha, beta carbon shifts of 7-11 residues.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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