3IKR

Crystal structure of alpha 1-4 mannobiose bound trimeric human lung surfactant protein D

Summary for 3IKR

• Entry DOI: 10.2210/pdb3ikr/pdb
• Related: 1pw9 1pwb 3ikn 3ikp 3ikq
• Descriptor: Pulmonary surfactant-associated protein D, CALCIUM ION, alpha-D-mannopyranose, ... (4 entities in total)
• Functional Keywords: trimeric recombinant fragment, neck+crd, collagen, disulfide bond, extracellular matrix, gaseous exchange, glycoprotein, hydroxylation, lectin, secreted, surface film, sugar binding protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 3
• Total formula weight: 57446.12

Authors

Shrive, A.K.,Greenhough, T.J. (deposition date: 2009-08-06, release date: 2009-11-17, Last modification date: 2023-11-01)

Primary citation

Shrive, A.K.,Martin, C.,Burns, I.,Paterson, J.M.,Martin, J.D.,Townsend, J.P.,Waters, P.,Clark, H.W.,Kishore, U.,Reid, K.B.M.,Greenhough, T.J.
Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325
J.Mol.Biol., 394:776-788, 2009

PubMed Abstract: The crystal structures of a biologically and therapeutically active recombinant homotrimeric fragment of human lung surfactant protein D with a series of bound ligands have been determined. While the structures reveal various different binding modes, all utilise a similarly positioned pair of mannose-type O3' and O4' hydroxyls with no direct interaction between any non-terminal sugar and protein. The orientation, position, and interactions of the bound terminal sugar depend on the sugar itself, the presence and form of glycosidic linkage, and the environment in the crystal, which, via Asp325, places stereochemical and electronic constraints, different for the three different subunits in the homotrimer, on the ligand-binding site. As a direct consequence of this influence, the other binding-pocket flanking residue, Arg343, exhibits variable conformation and variable interactions with bound ligand and leaves open to question which orientation of terminal mannobiose, and of other terminal disaccharides, may be present in extended physiological ligands. The combined structural evidence shows that there is significant flexibility in recognition; that Asp325, in addition to Arg343, is an important determinant of ligand selectivity, recognition, and binding; and that differences in crystal contact interfaces exert, through Asp325, significant influence on preferred binding modes.

PubMed: 19799916
DOI: 10.1016/j.jmb.2009.09.057

Experimental method

X-RAY DIFFRACTION (1.65 Å)