Research Guides: Biochemistry Research Guide: Protein Domains and Macromolecular Structures

Protein Domains and Macromolecular Structure

Protein Domain and Macromolecular Structure

Conserved Domains and Protein Classification

CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins. These are available as position-specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via RPS-BLAST. CDD content includes NCBI-curated domains, which use 3D-structure information to explicitly define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAMs).

How to use the conserved domain resources: examples

Identify the putative function of a protein sequence

Identify a protein's classification based on domain architecture

Identify the amino acids in a protein sequence that are putatively involved in functions such as binding or catalysis, as mapped from conserved domain annotations to the query sequence

View a query protein sequence embedded within the multiple sequence alignment of a domain model

Interactively view the 3D structure of a conserved domain

Find other proteins with similar domain architecture

Interactively view the phylogenetic sequence tree for a conserved domain model of interest with or without a query sequence embedded

Macromolecular Structures

Molecular Modeling Database (MMDB)

Experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, computationally identified 3D domains (compact substructures) that are used to identify similar 3D structures, as well as links to literature, similar sequences, information about chemicals bound to the structures, and more. These connections make it possible, for example, to find 3D structures for homologs of a protein sequence of interest, then interactively view the sequence-structure relationships, active sites, bound chemicals, journal articles, and more.

How to use the macromolecular structures resources: examples

Retrieve structures for a gene/protein product of interest

Align a query protein to a similar sequence from a 3D structure and interactively view sequence/structure relationships

Retrieve 3D structures bound to a specific chemical (e.g., aspirin)

Interactively view a 3D structure and its corresponding sequence data to examine sequence-structure relationship

Find protein structures that are similar in 3D shape to a structure of interest, regardless of degree of sequence similarity

Compare a newly resolved 3D structure in PDB format against the 3D coordinates of known structures already in the public domain