Well I am sure they all do have a structure, the question is rather if we know the exact 3d structure ;) So. Check out PDBe (https://www.ebi.ac.uk/pdbe/) if you don't know it already, that might be a great resource to start. I never used their API but they have one, so with some scripting you might be able to check your data in 'one go'.

What do your "protein names" look like? If you have UniProt accession numbers or gene names, you can use the UniProt IDmapping tool at http://www.uniprot.org/uploadlists to map your identifiers or gene names to PDB.

Please don't hesitate to contact the UniProt helpdesk if you have any UniProt-specific questions.

If you have NCBI sequence identifier or can retrieve amino acid sequences from the name of proteins, you can use blastp in NCBI website. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome Select "Protein Data Bank protein" at the "Database" section. It can process multiple sequences at once (but might have some limitation).