Computational structural and mechanistic characterization of alanine dehydrogenase from Melghiribacillus thermohalophilus (MetAlaDH): homology models, docking poses, and interaction analyses

Description

This dataset supports the computational study of alanine dehydrogenase from the polyextremophile Melghiribacillus thermohalophilus (MetAlaDH; UniProt A0A4R3N762). It contains the hexameric homology model built with SWISS-MODEL using Geobacillus kaustophilus AlaDH (PDB 8HYH) as template, the AlphaFold 3 monomeric model, the eight docked protein-ligand complexes (apo, holo-NAD+ and holo-NADH states with pyruvate, L-alanine, NAD+ and NADH), the raw PLIP interaction reports for all complexes, the re-docking control files for the GkAlaDH 8HYH template, and the MetAlaDH protein sequence.

Steps to reproduce

1. Homology model: SWISS-MODEL (https://swissmodel.expasy.org) with MetAlaDH sequence (UniProt A0A4R3N762) and template PDB 8HYH chain A; hexameric biological assembly selected. 2. Monomeric cross-validation: AlphaFold 3 server (https://alphafoldserver.com). 3. Validation: PROCHECK, Verify3D and ERRAT via the SAVES v6.1 server (https://saves.mbi.ucla.edu). 4. Ligands: retrieved from PubChem in 3D SDF format, converted with AutoDockTools v1.5.6. 5. Docking: PyRx v0.8 with AutoDock Vina; 30 x 30 x 30 A grid centred on the active site; exhaustiveness 8; nine poses retained per run. 6. Interaction analysis: PLIP v2.4.0 (primary quantitative reference); LigPlot+ v2.3.1 and UCSF ChimeraX v1.12 for visualisation. 7. Re-docking control: pyruvate and NAD+ re-docked into 8HYH after removal of co-crystallised ligands (pyruvate exhaustiveness 8; NAD+ exhaustiveness 32).

Institutions

• Düzce Üniversitesi

  Düzce, Düzce

Categories

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