Heme Protein Database

April 24, 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.

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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.
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The Heme Protein Database includes the heme protein domain secondary structure classifications in CATH v3.0.0. The Figure at left gives a CATH wheel which shows that the dominant secondary structures for all structurally characterized heme proteins is mainly alpha helix (red wedges). Hemes in mixed alpha-beta (yellow) and mostly beta (green) domains are less prevalent and only a single heme protein, NapB, binds its hemes in a domain with little secondary structure (blue).