Protein superfamily members as targets for computer modeling: the carbohydrate recognition domain of a macrophage lectin.
Members of protein superfamilies display similar folds, but share only limited sequence identity, often 25% or less. Thus, it is not straightforward to apply standard homology modeling methods to construct reliable three-dimensional models of such proteins. A three-dimensional model of the carbohydrate recognition domain of the rat macrophage lectin, a member of the calcium-dependent (C-type) lectin superfamily, has been generated to illustrate how information provided by comparison of X-ray structures and sequence-structure alignments can aid in comparative modeling when primary sequence similarities are low.
Stenkamp
R E
RE
Department of Biological Structure, University of Washington, Seattle 98195, USA. stenkamp@u.washington.edu
Aruffo
A
A
Bajorath
J
J
D000595:Amino Acid Sequence; D000818:Animals; D001212:Asialoglycoproteins; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019040:E-Selectin / Q000737:chemistry; D037102:Lectins / Q000737:chemistry*; D037181:Lectins, C-Type; D008264:Macrophages / Q000378:metabolism; D037241:Mannose-Binding Lectins; D008565:Membrane Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D051381:Rats; D011956:Receptors, Cell Surface; D016415:Sequence Alignment; D013816:Thermodynamics
D001212:Asialoglycoproteins; D002352:Carrier Proteins; C023339:Clec10a protein, rat; D019040:E-Selectin; D037102:Lectins; D037181:Lectins, C-Type; D037241:Mannose-Binding Lectins; D008565:Membrane Proteins; D011956:Receptors, Cell Surface