What is a .PDB file?
It depends. 2 unrelated formats use the .pdb extension, so the name alone cannot tell you what you have. The bytes can: each format below starts differently, and dropping the file on our detector settles it in a second without uploading anything.
Windows Program Database
Binary · MIME type application/octet-stream
How to recognise it: starts with 4D 69 63 72 6F 73 6F 66 74 20 43 2F 43 2B 2B 20 4D 53 46 20 37 2E 30 30 (Microsoft C/C++ MSF 7.00).
Protein DB
Data · MIME type chemical/x-pdb
Why one extension, several formats
Extensions are a convention, not a registry. Any program can claim any three or four letters, and when two did so independently, both stuck. Operating systems resolve the clash by file association, so a double-click opens whichever application last registered .pdb, which may be the wrong one. Looking at the first bytes removes the guesswork: a format's signature is fixed by its specification, while its extension is whatever the file was last named.
Check it from a terminal
# macOS and Linux
xxd -l 16 file.pdb
file file.pdb
# Windows PowerShell
Format-Hex -Path file.pdb -Count 16