[English] 日本語
Yorodumi- PDB-1i93: NMR ENSEMBLE OF ION-SELECTIVE LIGAND D16 FOR PLATELET INTEGRIN AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i93 | ||||||
---|---|---|---|---|---|---|---|
Title | NMR ENSEMBLE OF ION-SELECTIVE LIGAND D16 FOR PLATELET INTEGRIN ALPHAIIB-BETA3 | ||||||
Components | ION-SELECTIVE LIGAND D16 | ||||||
Keywords | CELL ADHESION / INTEGRIN / RGD | ||||||
Method | SOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, CHEMICAL SHIFT REFINEMENT. | ||||||
Authors | Smith, J.W. / Le Calvez, H. / Parra-Gessert, L. / Preece, N.E. / Jia, X. / Assa-Munt, N. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i93.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i93.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i93_validation.pdf.gz | 339.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1i93_full_validation.pdf.gz | 418.3 KB | Display | |
Data in XML | 1i93_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 1i93_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i93 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i93 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | 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 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Type: NOESY & DQF-COSY |
NMR details | Text: THE ENSEMBLE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES (CIRCA 2000) |
-Sample preparation
Details | Contents: 3MG D16/ML |
---|---|
Sample conditions | Ionic strength: 10mM PHOSPHATE/5% D2O / pH: 6.50 / Pressure: 1 atm / Temperature: 278.00 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: 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 ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 15 |