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Yorodumi- PDB-1d7t: NMR STRUCTURE OF AN ENGINEERED CONTRYPHAN CYCLIC PEPTIDE (MOTIF C... -
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-Basic information
Entry | Database: PDB / ID: 1d7t | ||||||
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Title | NMR STRUCTURE OF AN ENGINEERED CONTRYPHAN CYCLIC PEPTIDE (MOTIF CPXXPXC) | ||||||
Components | YNK-CONTRYPHAN | ||||||
Keywords | DE NOVO PROTEIN / DISULFIDE BOND / D-HANDED / BETA TURN / CIS PROLINE | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING | ||||||
Authors | Pallaghy, P.K. / Norton, R.S. | ||||||
Citation | Journal: Biopolymers / Year: 2000 Title: The cyclic contryphan motif CPxXPXC, a robust scaffold potentially useful as an omega-conotoxin mimic. Authors: Pallaghy, P.K. / Norton, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d7t.cif.gz | 43.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d7t.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 1d7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d7t_validation.pdf.gz | 353.7 KB | Display | wwPDB validaton report |
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Full document | 1d7t_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 1d7t_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1d7t_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d7t ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d7t | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 897.054 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE SEQUENCE WAS DESIGNED TO MIMIC THE SURFACE OF W-CONOTOXIN GVIA FROM CONUS GEOGRAPHUS AND IS BASED ON THE CONTRYPHAN-R SCAFFOLD FROM CONUS RADIATUS Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. |
-Sample preparation
Details | Contents: 21 MM YNK-CONTRYPHAN |
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Sample conditions | Ionic strength: 0 / pH: 3.5 / Pressure: AMBIENT / Temperature: 283 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software | Name: X-PLOR / Version: 3.5 / Developer: BRUNGER / Classification: refinement |
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Refinement | Method: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1 Details: STRUCTURES ARE BASED ON 104 NOES AND 2 PHI-ANGLES AND 4 CHI1-ANGLES. |
NMR representative | Selection criteria: closest to the average |
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20 |