2KAW
NMR structure of the mDvl1 PDZ domain in complex with its inhibitor
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_13C-F1_HALF_FILTERED_F2_EDIT | 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 | 7.5 | AMBIENT | 293 | |
2 | 2D 1H-15N HSQC | 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 | 7.5 | AMBIENT | 293 | |
3 | 2D 1H-13C HSQC | 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 | 7.5 | AMBIENT | 293 | |
4 | 3D CBCA(CO)NH | 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 | 7.5 | AMBIENT | 293 | |
5 | 3D HNCO | 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 | 7.5 | AMBIENT | 293 | |
6 | 3D CBCA(CO)NH | 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 | 7.5 | AMBIENT | 293 | |
7 | 3D HCCH-TOCSY | 1MM MDVL1 PDZ DOMAIN U-15N,13C, 10 MM SUZ, 100MM PHOSPHATE BUFFER PH 7.5, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100 | 7.5 | AMBIENT | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 800 |
3 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, HADDOCK | NOE distance violation (<0.5A) | HADDOCK |
NMR Ensemble Information | |
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Conformer Selection Criteria | LOWEST ENERGY CONFORMATION |
Conformers Calculated Total Number | 2000 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | THE STRUCTURE WAS DETERMINED WITH HADDOCK USING BASED ON A TOTAL OF 55 RESTRAINTS: 45 INTERMOLECULAR DISTANCE CONTRAINTS, 7 INTRAMOLECULAR DISTANCE CONTRAINTS FOR SMALL MOLECULE, AND 3 ARE DISTANCE RESTRAINTS FROM HYDROGEN BONDS |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | HADDOCK | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | structure solution | HADDOCK | 1.2 | Dominguez, Boelens, Bonvin |
3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | chemical shift assignment | SPAKY | 3.1 | Goddard |
5 | refinement | HADDOCK | 1.2 | Dominguez, Boelens, Bonvin |