Structure of a lignin peroxidase ligand access channel-atrazine docking complex

Published: 15 Apr 2018 | Version 2 | DOI: 10.17632/dvjms8448j.2
Contributor(s):
  • János Ecker,
    Unspecified
    Szent Istvan University Faculty of Agricultural and Environmental Sciences
  • László Fülöp
    László Fülöp
    Szent Istvan University Faculty of Agricultural and Environmental Sciences

Description of this data

State of the lignin peroxidase-atrazine complex after molecular docking. The conformer used in docking was created at 298 K temperature in a 10 ns long molecular dynamics simulation. The input structure for molecular dynamics was obtained from the RCSB PDB database (1B82). Docking was performed with DockingServer, molecular dynamics was performed with Nanoscale Molecular Dynamics (NAMD) software (CHARMM36 force field).

Experiment data files

Steps to reproduce

  1. PDB database id: 1B82

  2. NAMD software: Energy minimization (20-30 ps).

  3. NAMD software: Molecular dynamics after solvation and neutralization (298 K, NPT ensemble, Periodic Boundary Conditions and Particle Mesh Ewald electrostatics, CHARMM36 force field, Duration: 10 ns).

  4. DockingServer: 20*20*20 Å sized Simulation Box, ligand preparation for atrazine molecule, Gasteiger method for charge calculation, ga_run value: 255. Center of the Simulation Box was the His82 residue.

Related links

Latest version

  • Version 2

    2018-04-15

    Published: 2018-04-15

    DOI: 10.17632/dvjms8448j.2

    Cite this dataset

    Ecker, János; Fülöp, László (2018), “Structure of a lignin peroxidase ligand access channel-atrazine docking complex”, Mendeley Data, v2 http://dx.doi.org/10.17632/dvjms8448j.2

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Institutions

Szent Istvan University Faculty of Agricultural and Environmental Sciences

Categories

Three-Dimensional Graphics, Enzyme Structure, Enzyme Structure-Function Relationship, Ligand Binding, Molecular Docking, Three-Dimensional Reconstruction of Biomoleculair Structures

Licence

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