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Solution structure of a lactam analogue (DabD) of HIV gp41 600-612 loop.
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
DQF-COSY
3,5 mM peptide in 500ul DMSO-D6
DMSO-D6
ambient
298
2
2D NOESY
3,5 mM peptide in 500ul DMSO-D6
DMSO-D6
ambient
298
3
TOCSY
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
400
2
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
Torsion angle dinamics, molecular dynamics, energy minimization.
50 INITIAL RANDOM STRUCTURES WERE GENERATED USING SIMULATED ANNEALING IN DYANA SOFTWARE, FOLLOWED BY 500PS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K, 200 PS MD UNDER NMR RESTRAINTS AND 750 STEPS CONJUGATED GRADIENT EM USING DISCOVER OF MSI SOFTWARE
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
target function
Conformers Calculated Total Number
50
Conformers Submitted Total Number
49
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
This structure was determined using standard 2D homonuclear techniques. Different NOESY experiments with mixing times from 80 ms to 800 ms were recorded, in order to determined the best conditions avoiding spin diffusion.
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
collection
XwinNMR
2.6
Bruker GMBH
2
processing
XwinNMR
2.6
Bruker GMBH
3
data analysis
XEASY
1.2
Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10
4
refinement
DYANA
1.5
Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol. 273, 283-298