Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
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3 months ago
4fzcgueyp5 • 0

I need a small protein that has multiple chains, but the total number of atoms will not be more than fifty.

I need this to experiment with in my software.

Can you suggest such a protein PDB?

protein pdb protein-databank • 757 views
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This is a perfect example of a question that you can ask one of the AI chatbots. Insulin may fit but it will have 60 AA.

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I asked GPT4. There was no name given.

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There's a 'Chain size' entry on the search form on OCA, here under 'Additional searches' towards the bottom of the Search page, that would help you explore the many options. It allows setting ranges and 'less than' settings.
Unfortunately, it doesn't also have an option for number of chains, however, it may make for a starting point to further explore.
OCA makes it easy to browser PDB entries and summarizes reports regularly, see here.
REFERENCE: Prilusky, J. (1996), "OCA, a browser-database for protein structure/function." URL http://oca.weizmann.ac.il and mirrors worldwide.

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3 months ago

using sparql uniprot:https://sparql.uniprot.org/

prot                                        n_chains
http://purl.uniprot.org/uniprot/A0A0B5A7M7  "2"
http://purl.uniprot.org/uniprot/A0A0B5A7N1  "2"
http://purl.uniprot.org/uniprot/A0A0B5A7N5  "2"
http://purl.uniprot.org/uniprot/A0A0B5A7N8  "2"
http://purl.uniprot.org/uniprot/A0A0B5A7P2  "2"
http://purl.uniprot.org/uniprot/A0A0B5A8P4  "2"
http://purl.uniprot.org/uniprot/A0A0B5A8P8  "2"
http://purl.uniprot.org/uniprot/A0A0B5A8Q2  "2"
http://purl.uniprot.org/uniprot/A0A0B5A8Q6  "2"
....
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Pierre Lindenbaum Additional requirement is that the protein be < 50 AA total (including both chains). Can you add that limit to this query?

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it's already here ( I put 60 instead of 50)..

  FILTER(   strlen(str(?pep)) > 60 ) .
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I am really impressed by this answer and will bookmark it, in case I ever need to search PDB. However, the original post asks for 50 atoms and not 50 amino acids.

You are probably correct to assume that 50 amino acids were sought after, since a glycine dipeptide already has 5 carbon atoms, 2 nitrogen atoms, 2 oxygen atoms and 10 hydrogen atoms = 19 atoms in total. A H-bonded Dicysteine C6 H14 N2 O4 S2 = 28 atoms, when oxidized as Cystine 26 atoms. Glutathione already has C10 H17 N3 O6 S = 37 atoms.

But nothing in that range would be considered a protein or peptide hormone...

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