Sandbox Reserved 689

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(Rifampicin crystal structure from Nakashima, et al. 2011)
(Rifampicin crystal structure from Nakashima, et al. 2011)
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'''Minocycline''' is a lower molecular weight drug (~400 g/mol) that has been crystallized in the <scene name='Sandbox_Reserved_689/Minocycline_acrb_binding/7'>distal binding pocket</scene>.
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'''Minocycline''' is a lower molecular weight drug (~400 g/mol) that has been crystallized in the <scene name='Sandbox_Reserved_689/Minocycline_acrb_binding/6'>distal binding pocket</scene>.
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<scene name='Sandbox_Reserved_689/Minocycline_acrb_binding_sl/1'>behind the switch loop</scene> (switch loop shown in green)
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<scene name='Sandbox_Reserved_689/Minocycline_acrb_binding/3'>Polar and Nonpolar</scene> (blue=polar, green=aliphatic, orange=hydrophobic).
== Energy Transduction ==
== Energy Transduction ==
There are <scene name='Sandbox_Reserved_689/Proton_translocation_residues/1'>Four Titrateable Residues</scene> (Asp408, Asp407, Lys940, and Arg 971) whose protonation and deprotonation are suggested to play a large role in the conformational change between the L, T, and O states (Eicher, et al. 2009). PDB: 3D9B
There are <scene name='Sandbox_Reserved_689/Proton_translocation_residues/1'>Four Titrateable Residues</scene> (Asp408, Asp407, Lys940, and Arg 971) whose protonation and deprotonation are suggested to play a large role in the conformational change between the L, T, and O states (Eicher, et al. 2009). PDB: 3D9B

Revision as of 15:52, 30 April 2013

This Sandbox is Reserved from 30/01/2013, through 30/12/2013 for use in the course "Biochemistry II" taught by Hannah Tims at the Messiah College. This reservation includes Sandbox Reserved 686 through Sandbox Reserved 700.
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Contents

The E. coli AcrB Efflux Pump

Structure

The AcrB efflux pump is part of a tripartite system used by E. Coli to remove antibiotic and other toxic molecules from the bacterial cell.

Asymmetrical AcrB

Drag the structure with the mouse to rotate


Structural Elements


Substrates

Because of the large binding pockets in AcrB, it is able to bind and export a wide variety of antibiotic drugs and other toxins.

Rifampicin is a high molecular weight drug (~800 g/mol) that has been crystallized in the proximal binding pocket

, interacting residues (all residues within 4 Angstroms) highlighted and shown in ball-and-stick representation.

interacting residues are shown here (Polar in blue, nonpolar in orange).

(switch loop is shown in orange).

(Rifampicin crystal structure from Nakashima, et al. 2011)

Minocycline is a lower molecular weight drug (~400 g/mol) that has been crystallized in the .


(switch loop shown in green)

(blue=polar, green=aliphatic, orange=hydrophobic).

Energy Transduction

There are (Asp408, Asp407, Lys940, and Arg 971) whose protonation and deprotonation are suggested to play a large role in the conformational change between the L, T, and O states (Eicher, et al. 2009). PDB: 3D9B

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