I'm trying to use EzMol to illustrate a protein sequence, but there are no PDB files for the sequence I'm trying to analyze. (NCBI: XP_006501616.1)
How can I create a PDB file?
You can generate a CSM (computed structural model). It is a prediction, and eventually you need an experimental way to prove it is a correct model. But the trend is to use the prediction in the hypothesis stage.
This video demonstrates how you can generate a PDB with only sequence by ESMFold.
https://youtu.be/CG_dS4Nhm8s
As you have already noted, there isn't an entry in the PDB database bearing significant identity (>40%) and coverage (>70%) to you sequence of interest. There are a few PDB entries that bear around 28% identity and about 32% coverage to your sequence. You may try predicting the 3D structure using I Tasser (https://zhanggroup.org/I-TASSER/), although I think Alpha Fold (https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb) will do a better job in this scenario.
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