How to use ZincBind
There's a particular zinc binding site I want to examine.
If you know the PDB code of the structure containing your zinc binding site, you can access it by entering the PDB code into the search bar on the main page. This should return the PDB, and all of the zinc sites it contains.
You can click the PDB to go to the page for that PDB and view all of its contents, or if you see the specific site you are looking for in the search results, you can click that to go directly to it.
I don't have a particular binding site in mind, but I am looking for a particular kind of binding site.
The advanced search page allows you to query the data by some particular parameter. For example, you could look at only those structures with a resolution better than 1.5 Angstroms, or those which describe themselves as a zinc finger, or NMR structures published since 2015 from yeast.
I have a peptide sequence and I want to know if it encodes a protein which binds zinc.
Currently the way to get an idea of whether your sequence binds zinc is to run it through ZincBind's BLAST search utility, at the bottom of that page.
This will tell you how similar your sequence is to sequences known to bind zinc, and results are returned 'best match first'. More sophisticated tools are planned for the future.
You can pass in a raw peptide sequence, or a FASTA formatted peptide sequence.
I'm a developer and I want to access the data with a script or other program.
I don't have a particular goal in mind, I just want to see what kind of data is here.
The full list of binding sites can be browsed here.
In addition, you can browse by family here. In ZincBind, a family is a collection of binding sites that each share the same residue identities. So, the 'H3' family contains all those which contain three histidine residues, 'C2H2' contains all those with two cysteine and two histidine residues, and so on.
I'm on the page for a PDB and I don't know what I'm looking at.
At the top of the page is the PDB's title - this is how the structure as a whole is described in the .pdb file. It may or may not mention zinc - a structure's zinc binding sites are not always the most important feature after all.
Next comes a table of descriptive properties of the PDB - when it was deposited to the Data Bank, how its structure is classified, etc. These are parsed automatically from the .pdb file.
After this is a description of the 'zinc bearing chains' in the PDB - these are those chains with residues involved in zinc binding in some way - and the relevant metal ions it contains. Here 'relevant' means zinc, and any other metal that is in a zinc binding site. Within the chain sequence, binding residues will be capitalised and in bold.
Any zinc atoms in the PDb which have not been assigned a binding site will also be listed, along with the reason for their exclusion.
Then there is a list of all the zinc binding sites in that PDB. Each one is a clickable link to that site's page, and has a summary of the residues in that site.
Finally there is a 3D manipulatable view of the whole PDB structure, with all the zinc binding sites visible. You can manipulate this with your mouse/touch gestures, and use the controls that accompany it.
I'm on the page for a Zinc Site and I don't know what I'm looking at.
At the top of the page is the Zinc Site's unique ID - this is generally the PDB code that contains it followed by the zinc site number within that protein.
After this is a quick summary of the binding site - the title of the PDB it comes from, and the IDs of the metals and residues it contains. You can click on any of these boxes, and the relevant atoms will light up in green in the 3D display below.
Next comes links to any 'equivalent' binding sites. Many proteins are duplicated in the PDB, or exist in mutated forms, so many zinc binding sites will be duplicates. These are clustered together in ZincBind by first clustering all chains into clusters on 90% sequence identity, and then assigning sites to clusters where all sites in that cluster are associated with the same chain cluster(s), and have the same residue IDs. Clicking any of these links will take you to a page for a zinc site which looks very similar.
Below this is the 3D manipulatable view of the site, zoomed in to the relevant residues. You can manipulate this with your mouse/touch gestures, and use the controls that accompany it.
Then there is a list of chains associated with the binding site. Binding residues are highlighted here, but only if they are binding in this particular site.
Finally there is a summary of the other relevant PDB information for the structure the site comes from.
I'm on the page for a Zinc Site Group and I don't know what I'm looking at.
The group's family will be listed first, along with classifications and keywords that appear often in the binding sites within this group. These can often give an insight as to the common function of the sites in the group, but do remember that they are automatically generated.
After this comes a list of binding sites in this group.