There are different PDB IDs for one protein in literature. For example, in case of NF-kappa-B protein, I have found three different PDB IDs so far. How can I decide which one to select and use in my molecular docking studies?
Thanks
Look at all of them, superimpose them in a molecular viewer - If there are clear conformational differences, you may want to use multiple structures. On the other hand, if they are essentially the same, you use the one with the best resolution and completeness. As NFkappa B is a large protein with several folded domains interspersed by flexible stretches (see https://alphafold.ebi.ac.uk/entry/P19838 for NFKB1_HUMAN https://www.uniprot.org/uniprotkb/P19838/entry ) forming homo- and heterodimers, and experimental structures only representing parts of the full sequence, you will have to decide which part of the molecule you want to study based on the function of these domains.
Based on the resolution (< 2 Å) you can select and on the basis of co-crystal ligand bind to that protein as well as stds compound binding into it and involvement of amino acids.
Sometimes different ligands are associated with proteins and they are categorized under different PDB IDs. Additionally, you can scroll down and get to know the details of the structure with respect to chains and conformation. Thoroughly go through published literature to download your required protein.
The most optimal way could be done by ensemble docking. To my knowledge GOLD and Glide have the former option.
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