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Amber scripts to simulate a homology model of a berberine-bridge enzyme and its substrate

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Chebuu/A6P6V9-model

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Homology model of UniProt ID A6P6V9 (~85% sequence identity 3VTE).

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A6P6V9-asite/

  • H292
    • Catalytic residue
    • Minimized pose w/o substrate
    • Protonated (HID)
  • Y484
    • Catalytic residue
    • Minimized pose w/o substrate
    • Protonated (-OH)
  • FHC
    • FAD cofactor
    • Minimized pose w/o substrate
    • Covalent H114, C176
    • Protonated (semiquinone)
  • CBGA
    • Substrate
    • Conformer placed by hand
    • Protonated (-COOH)

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Amber scripts to simulate a homology model of a berberine-bridge enzyme and its substrate

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