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Annemarie Honegger Popular answer

It is also possible that the resolution was not sufficient to unambiguously align the sequence to the structure. If it is a natural protein, compare the sequence derived from the structure to the UniProt sequence.

Vivek Dhar Dwivedi

It may be an unknown ligand. If it is unknown amino acid then you can use SAS server or profunc server for its annotation. Or you can send me this file for analysis.

Annemarie Honegger

Sneha Pasupati

Probably they should be some unknown ligand as told by Vivek. You can see their structure using visualisation softwares like PyMOL.