Heme Protein Database

July 22, 2014
 

Welcome to The Heme Protein Database

The Heme Protein Database couples structural information on a non-redundant set of heme proteins with their associated electrochemical midpoint reduction potential values. The HPD incorporates the structural data on heme proteins in the RCSB Protein Data Bank (PDB) with the protein structure classifications in CATH 3.0.0 and electrochemical data from the primary literature. The data are presented along with MOLMOL images of the heme proteins and links to the Prosthetic Groups and Metal Ions in Protein Active Sites Database, PROMISE.

This heme protein structure-function database may be searched in one of the three ways presented at left. The Search by PDB ID feature allows the user to identify the properties of an individual heme protein. Data on sets of heme proteins can be retrieved using either the Detailed Search Function, which yields a list of all the individual members of the set, or the Global View function, which compiles the data on all the members of the set as a group.

110

Search by PDB ID  

Detailed Search

Global View

Secondary structure

Heme type
Coordination Number
Axial Ligands
Reduction Potential Range
to
Run Search

In citing the Heme Protein Database, please refer to:

Reedy, C.J.; Elvekrog, M.M.; Gibney, B.R. (2008) Development of a heme protein structure-electrochemical function database. Nucleic Acids Research, D307-D313.
[PDF]

3.jpg
The Heme Protein Database includes 157 heme protein reduction potential values culled from the primary scientific literature. The highest potential heme in the HPD is the His/Met coordinated c-type heme in diheme cytochrome c peroxidase at +450 mV vs. SHE; the lowest potential heme is the His/Tyr ligated heme b in HasA at -550 mV vs. SHE. The Figure at left gives the range of reduction potential values of hemes bound to protein domains by secondary structure type. The arrows give the ranges for all secondary structures (black), alpha-helical domains (red), beta-sheet (yellow), mixed alpha-beta (green) and little secondary structure (blue)