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C5. Structual Clases of Proteins

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  • Proteins can be divided into 3 classes of protein, depending on their characteristic secondary structure. Click below for Chime structures showing examples of these proteins.

    • alpha proteins - consist of predominately alpha helix.

    Jmol: Updated cytochrome B562 Jmol14 (Java) | JSMol (HTML5)

    Jmol: Updated met-myoglobin Jmol14 (Java) | JSMol (HTML5)

    • alpha/beta proteins - consist of a common of alpha and beta structure. These are the most common class.

    Jmol: Updated triose phosphate isomerase Jmol14 (Java) | JSMol (HTML5)

    Jmol: Updated hexokinase Jmol14 (Java) | JSMol (HTML5)

    • beta proteins - consist of predominantly beta structure.

    Jmol: Updated superoxide dismutase Jmol14 (Java) | JSMol (HTML5)

    Jmol: Updated human IgG1 antibodyJmol14 (Java) | JSMol (HTML5)

    Jmol: Updated retinol binding proteinJmol14 (Java) | JSMol (HTML5)

    fatty acid binding proteins; Peptide-N(4)-(N-Acetyl-b-D-Glucosaminyl) Asparagine Amidase (PNGase F) - under construction.

    A more complete classification of protein structure has been developed based on the following hierarchy of organization: Class, Architecture, Topology, and Homologous Superfamilies - CATH.

    • Class: the highest level of organization which consists of four classes - mainly alpha, mainly beta, alpha-beta, and few secondary structures
    • Architecture (40 types): describes the shape of domain based on secondary structures but doesn't describe how they are connected. Ex: beta barrel, beta propellor
    • Topology (or fold group, 1233 types): members in topology groups have a common fold or topology in the "core" of the domain structure.
    • Homologous Superfamilies (2386 types): These groups are homologous in sequence or structure and derive from a common precursor gene/protein.

    Structural Biology Knowledge Base

    Here are some 3D structures resources, accessible through a sequence or ID-based search. and collated in Nature's Structural Biology Knowledge Base.

    • Biological Magnetic Resonance Data Bank

    • CATH - structural classification of manually curated classification of protein domain structures

    • DisProt - Database of Protein Disorder

    • Gene3D - CATH domain assignments for protein sequences

    • NESG Functional Annotation Database - Computational analysis of function of protein of unknown function

    • Membrane proteins of known 3D structure

    • RCSB PDB - Protein Data Bank USA

    • PDBe - Protein Databank Europe

    • PDBj - Protein Databank Japan

    • PDBsum - a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank

    • PROCOGNATE - database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam

    • SCOP - Structural Classification of Proteins: detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structures are known

    • SMART (Simple Modular Architecture Research Tool) - allows the identification and annotation of genetically mobile domains and the analysis of domain architectures