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Here we have a 3D model of a sequence that match with this sequence VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK in Blast

the 3D structure is here

Why is there a chloride ion in this 3D model?

screenshot of the 3D structure

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It is a crystallisation artefact. Namely, the protein are placed in a condition where they fall out of solution without aggregating a gloop (as happens in most well in xstal trial) and to pack as a crystal they need to be placed nice and orderly. It is coordinated by water so is not relevant. A lot of structures have these —DMSO and ions are the most commonly.

Two footnotes.

  • 1ZV7 is a crystal structure, i.e. solved by X-ray diffraction. A model is generally used to described an in silico model, such as those from Swissmodel, phyre, I-Tasser etc. These are generated ab initio (from scratch) or threaded (mapped on top of) against crystal/EM/NMR structures. For Covid I-Tasser has a nice picture of its models.
  • The best source of info about structures is the PDB. RCSB PDB is more commonly used, while PDBe is more tricker to navigate (or used to be). Both have the same data, but are better for the extras than NCBI.
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