Results for 6c0v

PDB: 6c0v Gene name: ABCB1 UniProt: MDR1_HUMAN EMD: emd_7325.gz

Membrane mimetics: micelle; fluorinated Fos-Choline-8 Note: More manual adjustment needed because of the noise level

Cross-sections at different angles

green: density, gray dots: atoms from the all-atom model, lines: membrane boundaries defined by TMDET

The determined edges at each slice and their comparison to TMDET

dots: edges of the gradient, triangles: outliers,
dashed and solid lines: membrane boundaries defined by TMDET and MemBlob ( mean(Zi) decreased by the thickness of the interface region (8 Å))
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Manual settings applied

* end0 around -25 5
0-120 end1 around 20 5
130-350 end1 around 25 3

Boundary values (averages for MemBlob)

Z (PDBTM) Z (MemBlob) Z - 8
End1 16.75 23.17 15.17
End0 -16.75 -27.83 -19.83

Mapping the results to the structure

You can move/scale/rotate the structure. Blue: a.a. facing to bulk water; magenta: interface region; green: a.a. interacting with the hydrophobic membrane core; yellow: burried a.a. red: a.a. with an invisible side chain and non-protein molecules, for which DSSP cannot return SASA
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