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

Published: 15 April 2018| Version 2 | DOI: 10.17632/dvjms8448j.2
Contributors:
János Ecker,
László Fülöp

Description

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).

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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.

Institutions

Szent Istvan Egyetem Mezogazdasag- es Kornyezettudomanyi Kar

Categories

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

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