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- PDB-1i93: NMR ENSEMBLE OF ION-SELECTIVE LIGAND D16 FOR PLATELET INTEGRIN AL... -

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Basic information

Entry
Database: PDB / ID: 1i93
TitleNMR ENSEMBLE OF ION-SELECTIVE LIGAND D16 FOR PLATELET INTEGRIN ALPHAIIB-BETA3
ComponentsION-SELECTIVE LIGAND D16
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 17, 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 1.4Nov 20, 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:
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Assembly

Deposited unit
A: ION-SELECTIVE LIGAND D16


Theoretical massNumber of molelcules
Total (without water)1,4611
Polymers1,4611
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 D16


Mass: 1460.777 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized: Commercial solid phase with cyclization with selective disulphide oxidation
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY & DQF-COSY
NMR detailsText: THE ENSEMBLE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES (CIRCA 2000)

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Sample preparation

DetailsContents: 3MG D16/ML
Sample conditionsIonic strength: 10mM PHOSPHATE/5% D2O / pH: 6.5 / Pressure: 1 atm / Temperature: 278.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8.5.1 (CHEM.SHIFT.MODULE)BRUNGER A. NILGES M. (KUSZWESKI J. CLORE G.M.)refinement
VNMR6.1BVARIANINCcollection
Felix2000HARE,D. > Biosym > MSIdata analysis
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS, CHEMICAL SHIFT REFINEMENT.
Software ordinal: 1
Details: ENSEMBLE D16 IS BASED ON A TOTAL OF 74 NOE-DERIVED DISTANCE CONSTRAINTS, 9 DIHEDRAL ANGLE RESTRAINTS, 1 COVALENT CYS-SS-CYS BOND AND 1 LRGD, I, HYDROGEN BOND RESPECTIVELY. REFINEMENTS ...Details: ENSEMBLE D16 IS BASED ON A TOTAL OF 74 NOE-DERIVED DISTANCE CONSTRAINTS, 9 DIHEDRAL ANGLE RESTRAINTS, 1 COVALENT CYS-SS-CYS BOND AND 1 LRGD, I, HYDROGEN BOND RESPECTIVELY. REFINEMENTS INCORPORATED ALPHA PROTON AND ALPHA, BETA CARBON SHIFTS OF 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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