Metalloprotein Site Database and Browser - Packages

What will you find here?

Below you will find the raw data we have generated while automating the recognition of proteins containing metals (and other interesting elements). We are using a simple distance dependent algorithm to create a file containing the ligand atoms directly connected to the metal (the "ligands files"). We also generated site description files, which contain info on the site itself (one per metal in the protein), and eventually will contain more detailed geometrical info. Using the 2 files above and the PDB structure, we generated a "mini-PDB", which is a PDB formatted file containing only the metal and its ligands (first coordination sphere). From the mini-PDB files, we generated also VRML 2.0 files.

All these files are available as packages, i.e. in an achive (.tar.gz or .zip) containing all the individual files.

You are free to use these files, but The Scripps Research Institute retains the copyright for the data. If you want to contact us for questions or comments, send e-mail to: metallodb@scripps.edu, or use the e-mail link in the navigation bar.

File formats

Ligands file

The format of this file is as follows (space separated fields):
[PDB filename] [metal expr] [ligand1 expr] [ligand2 expr] ...
Where:

PDB filename: e.g. 1alj.pdb
metal expr: metal_symbol chain_ID residue_ID atom_symbol number_of_ligands, e.g. ZN A 451 ZN 4
ligandN exp: chain_ID residue_name residue_ID ligand_atom metal_ligand_distance, e.g. _ HIS 102 ND1 2.38
chain_ID: if not present we used "_", otherwise A|B|C|...

the metal_ligand_distance is in Angstroms.

Site description file

The name of each site description file is derivated from the PDB, the metal symbol and the site number in the particular protein. For example in the PDB file: 1hca.pdb, there is one Zn site, thus the generated file will be named: 1hca_zn1. This file will contain the following information:

name (the site description file name, e.g. 1hca_zn1)
file (the PDB structure used to generate the file, e.g. 1hca.pdb)
metal (symbol of the metal, e.g. zn)
short_description (e.g. 1hca.pdb ZN #1, res 1 ZN, 4 ligands)
center_chain (chain ID for the metal, e.g. _ or A or B ...)
center_res (residue number for the metal, e.g. 1)
center_atom (central atom, e.g. zn)
near_chain (comma separated chain IDs for the ligands, e.g. A,A,B,_)
near_res (comma separated residue numbers for the ligands, e.g. 90,86,110,33)

mini-PDB file

Extracted from the original PDB file. Contains the metal and its ligands as described in the site description file. Format is the same as the PDB, except for the headers, comments, etc.

VRML 2.0 file

Generated by using our program MV102 from the mini-PDB file, and contains a VRML representation suitable to be manipulated using any of the existing viewers.

PACKAGES (Updated: 2003/01/17)