InterMetalDB gathers intermolecular metal binding sites that are deposited in RCSB Protein Data Bank.
For every metal present in PDB structure coordinating environment is assessed within 3 Angstrom radius. If metal is coordinated by at least two heteroatoms from at least two different chains, metal is considered to be interfacialy bound. No other restraints like resolution requirements were applied.
Metal examination is based on biological assemblies as defined in PDB files. To build database is chosen assembly that has lowest energy while still holding an metal ion.
Representative metal binding sites are based on chain clustering on 50% sequence identity, and group identifier, which is based on metal coordinating environment in radius of 5 angstroms. Representative site is chosen based on best structure resolution.
Metal oxidation states presented in InterMetalDB are based on PDB files, thus such oxidation states should be taken with care, as they may be assumed rather than verified by an experimental means.
Knowing the PDB code of the structure containing intermolecularly bound metal you can view more detail about it by entering it in search field in Search for PDB structures. It will return PDB record. You can follow the link in order to see more details about PDB like: metal sites in PDB and structure visualization
You can query the data about PDB files by different parameters with Search for PDB structures, e.g. you can search for structures of human protein with resolution between 2.0-3 ansgtroms .
You can query the data about metal sites different parameters with Search for metal sites, e.g. you can search for metal sites that contain Zn(II) coordinated by four cysteines.
At top of the web page representing record there is a PDB title, next is PDB ID, that allow for downloading structure from RCSB Protein Data Bank. After that there are some more descriptive details regarding PDB file, when it was deposited, classification and keywords that help to find PDB record, technique that allowed for structure acquisition and more information. This description comes directly from RCSB PDB.
After PDB description are placed links to metal sites.
Web page representing metal site contains at the top id of corresponding PDB file, and metal site ID. Next comes information whether metal binding site is homomeric, and binding residues identifiers with corresponding chains.
At bottom of both web pages there is placed NGL viewer that allows for structure visualization.
Statistics webpage contains descriptive statistics of metal binding sites and PDB files gathered in InterMetalDB. This statistics allow to gain insight about metal ions bound in-between two macromolecules. At the top of the web site you can see different groups of amino acids or nucleotide residues involved in metal binding, by clicking on the group you will be redirected to search web site.
By clicking on a particular metal, you can learn about the lengths of bonds between ligands and metal, the amount of a particular metal relative to the presence of other ions, the most common coordination families, the most common ligands that coordinate the metal, and other useful information.
At the top of the web site you can see different groups of amino acids or nucleotide residues involved in metal binding, by clicking on the group you will be redirected to search web site.