2KS9
Solution conformation of substance P in water complexed with NK1R
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H TOCSY | 3.7 mM Substance P-1 | 90% H2O/10% D2O | minimum | 5.5 | ambient | 298 | |
| 2 | 2D 1H-1H NOESY | 3.7 mM Substance P-1 | 90% H2O/10% D2O | minimum | 5.5 | ambient | 298 | |
| 3 | 2D DQF-COSY | 3.7 mM Substance P-1 | 90% H2O/10% D2O | minimum | 5.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics, simulated annealing | Used for docking SP to NK1R, Used for modelling SP in XPLOR NIH; The structures are produced after docking using AUTODOCK using experimental NMR on Chain B | SPARKY-win32 |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 20 |
| Conformers Submitted Total Number | 5 |
| Representative Model | 1 (randomly chosen) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | SPARKY-win32 | Thomas Goddard | |
| 2 | structure solution | XPLOR-NIH | 2.17.0 | Charles Schwieters |
| 3 | structure solution | AutoDock | 4.0 | Arthur J.Olson |
| 4 | geometry optimization | XPLOR-NIH | 2.17.0 | Charles Schwieters |
| 5 | geometry optimization | AutoDock | 4.0 | Arthur J.Olson |
| 6 | refinement | AutoDock | 4.0 | Arthur J.Olson |
