9PDE | pdb_00009pde

Three-dimensional structure of kinase inhibitor Palbociclib-HIV TAR complex

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H TOCSY	0.9 mM HIV TAR RNA (29-MER)	90% H2O/10% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
2	2D 1H-1H NOESY	0.9 mM HIV TAR RNA (29-MER)	90% H2O/10% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
3	2D 1H-1H TOCSY	0.9 nM HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	298	Bruker AVANCE III 800
4	2D 1H-1H NOESY	0.9 nM HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	298	Bruker AVANCE III 800
5	2D 1H-1H TOCSY	0.9 mM HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
28	2D 1H-1H NOESY	0.9 mM HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
27	2D 1H-13C HMQC	0.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
26	2D 1H-13C CT-HSQC aliphatic	0.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
25	2D 1H-13C CT-HSQC aromatic	0.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
24	2D 1H-1H filtered NOESY	0.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	100% D2O	20 mM sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
23	2D 1H-15N HSQC	0.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
22	2D 1H-15N HSQC NH2 only	0.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
21	2D 1H-15N HNNCOSY	0.25 mM [U-99% 13C; U-99% 15N] HIV TAR RNA (29-MER)	95% H2O/5% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE II 600
20	2D 1H-1H TOCSY	0.9 mM [U-99% 2H] HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	298	Bruker AVANCE III 800
19	2D 1H-1H NOESY	0.9 mM [U-99% 2H] HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	298	Bruker AVANCE III 800
18	2D 1H-1H NOESY	0.9 mM [U-99% 2H] HIV TAR RNA (29-MER)	90% H2O/10% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800
17	2D 1H-1H TOCSY	0.35 mM [U-99% 2H] HIV TAR RNA (29-MER)	90% H2O/10% D2O	20 sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
16	2D 1H-1H NOESY	0.35 mM [U-99% 2H] HIV TAR RNA (29-MER)	90% H2O/10% D2O	20 sodium acetate mM	5.0	1 atm	298	Bruker AVANCE III 800
15	2D 1H-1H NOESY	0.35 mM [U-99% 2H] HIV TAR RNA (29-MER)	100% D2O	20 mM bis tris d19, 50 mM sodium chloride mM	5.8	1 atm	278	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE NEO	500
2	Bruker	AVANCE II	600
3	Bruker	AVANCE III	800

NMR Refinement
Method	Details	Software
simulated annealing		X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	200
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	processing	TopSpin		Bruker Biospin
3	chemical shift assignment	Sparky		Goddard
4	structure calculation	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
5	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore