Orbitals at a protein site
Find a sequence motif in any structure, or pick a bound ligand, cut it out with its metal and pocket, and draw the electron pairs that hold the site together: each ligand's lone pair and the zinc's empty 4s/4p orbitals that accept it. A ligand is also named as a molecule: its SMILES comes from the dictionary, from its name and from the geometry of its atoms, each route checked against the others, and opens on the other pages as a free molecule. The protein is never computed whole, so the cost depends on the site, not on the size of the protein. Structures come from a file or straight from a GL1X MolNFT record.
MolNFT collections: PDB Bank (v2, BinaryCIF on chain), PDB (v1) and AlphaFold (v1). AlphaFold models have no metals; the zinc is then placed from the motif.
PDB, PDBx/mmCIF or BinaryCIF, plain or gzip-compressed, up to 20 MB. Only the first model is read.
All from the PDB. 5A7U is the ADR1a zinc finger inside the ribosome tunnel (cryo-EM at 4.8 Å, with the NMR model 2ADR docked into it); 7DDO is ACE2 (cryo-EM at 3.4 Å). The other three open on a bound ligand; in 19HC every haem is bonded to two cysteines (haem c).
Find structures by ligand · GL1X ligand index
The index and the records are GL1X's; this page reads them in your browser. A binding site opens its record here, on that ligand.
Site report
Compute a site to see its geometry, protonation and metal bonds, or pick a ligand to see what molecule it is.