Structure of a lignin peroxidase ligand access channel-atrazine docking complex
Published: 26 Sep 2017
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Version 1
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DOI: 10.17632/dvjms8448j.1
Contributor(s):
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János Ecker,
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László Fülöp
László FülöpSzent 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 NAMD (CHARMM36 force field).
Experiment data files
Steps to reproduce
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PDB database id: 1B82
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NAMD software: Energy minimization (20-30 ps).
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NAMD software: Molecular dynamics after solvation and neutralization (298 K, 10 ns, NPT microcanonical ensemble, Periodic Boundary Conditions and Particle Mesh Ewald electrostatics, CHARMM36 force field).
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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.
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 NAMD (CHARMM36 force field).
Experiment data files
Steps to reproduce
-
PDB database id: 1B82
-
NAMD software: Energy minimization (20-30 ps).
-
NAMD software: Molecular dynamics after solvation and neutralization (298 K, 10 ns, NPT microcanonical ensemble, Periodic Boundary Conditions and Particle Mesh Ewald electrostatics, CHARMM36 force field).
-
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.
Latest version
Previous versions
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Version 1
2017-09-26
Published: 2017-09-26
DOI: 10.17632/dvjms8448j.1
Cite this dataset
Ecker, János; Fülöp, László (2017), “Structure of a lignin peroxidase ligand access channel-atrazine docking complex”, Mendeley Data, v1 http://dx.doi.org/10.17632/dvjms8448j.1
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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
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