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C5. Structual Clases of Proteins

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