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Solution structure of synthetic cyclic peptide mimicking the loop of HIV-1 gp41 glycoprotein envelope
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
2mM and 4mM peptide ; 500 ul DMSO-D6
DMSO-D6
ambient
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
400
2
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
torsion angle dynamics
energy minimisation
50 initial random strucutres were produced using simulated annealing in DYANA software.Refinement was done with 500 steps restrained minimization , 35ps MD in vacuo at 300K for equilibration and 200ps MD under NMR restraints and 750 steps conjugeted gradient EM using DISCOVER module of MSI software.
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
target function
Conformers Calculated Total Number
50
Conformers Submitted Total Number
1
Representative Model
1 (minimized average structure)
Additional NMR Experimental Information
Details
This structure was determined using standard 2D homonuclear techniques.
NOESY experiments with mixing times from 80ms to 800ms were reccorded in order to define the best conditions avoiding spin diffusion.
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
collection
XwinNMR
2.6
Bruker brmH
2
processing
XwinNMR
2.6
Bruker brmH
3
data analysis
XEASY
Bartels C.,Xia T. , Billeter M., Guentert P. and Wthrich K. J. Biomolecular NMR 5, 1-10
4
refinement
DYANA
1.5
Guentert P., Mumenthaler C.and Wuethrich K., (1997) J. Mol. Biol. 273, 283-298