Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
1.5mM peptide, 50mM phosphate buffer, pH 6.5
95% H2O/5% D2O
50mM phosphate buffer
6.5
ambient
278
2
2D TOCSY
1.5mM peptide, 50mM phosphate buffer, pH 6.5
95% H2O/5% D2O
50mM phosphate buffer
6.5
ambient
278
3
PE-COSY
1.5mM peptide, 50mM phosphate buffer, pH 6.5
95% H2O/5% D2O
50mM phosphate buffer
6.5
ambient
278
4
HSQC (1H-13C)-Dipsi-2(1H)
1.5mM peptide, 50mM phosphate buffer, pH 6.5
95% H2O/5% D2O
50mM phosphate buffer
6.5
ambient
278
5
HMQC (1H-15N) jr
1.5mM peptide, 50mM phosphate buffer, pH 6.5
95% H2O/5% D2O
50mM phosphate buffer
6.5
ambient
278
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DRX
600
2
Bruker
DRX
500
NMR Refinement
Method
Details
Software
Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFIS
NMRPipe
NMR Ensemble Information
Conformer Selection Criteria
Base set ensemble representative of the conformational space experimentally allowed
Conformers Calculated Total Number
6400
Conformers Submitted Total Number
81
Additional NMR Experimental Information
Details
Distance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance for MEDUSA were 600 and 100 kCal/mol respectively Clustering was performed with a cutoff of 1.0Angstrom A conformer was defined as different if either phi or psi angle for at least one aminoacid was differing by >15 degrees