PDBsum entry 3ikp

Sugar binding protein

PDB id: 3ikp

Contents

Protein chain

151 a.a. *

Ligands

IPD ×2

Metals

_CA ×10

Waters ×440

* Residue conservation analysis

PDB id:

3ikp

Name:

Sugar binding protein

Title:

Crystal structure of inositol phosphate bound trimeric human lung surfactant protein d

Structure:

Pulmonary surfactant-associated protein d. Chain: a, b, c. Fragment: unp residues 199-375. Synonym: sp-d, psp-d, lung surfactant protein d. Engineered: yes. Mutation: yes. Other_details: trimeric fragment of human lung surfactant protein d comprising alpha helical neck and carbohydrate recognition domains

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: sftpd, pspd, sftp4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.75Å R-factor: 0.198 R-free: 0.213

Authors:

A.K.Shrive,T.J.Greenhough

Key ref:

A.K.Shrive et al. (2009). Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325. J Mol Biol, 394, 776-788. PubMed id: 19799916 DOI: 10.1016/j.jmb.2009.09.057

Date:

06-Aug-09 Release date: 17-Nov-09

Protein chains

P35247  (SFTPD_HUMAN) -  Pulmonary surfactant-associated protein D from Homo sapiens

Seq: 375 a.a.

Struc: 151 a.a.

DOI no: 10.1016/j.jmb.2009.09.057

J Mol Biol 394:776-788 (2009)

PubMed id: 19799916

Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325.

A.K.Shrive, C.Martin, I.Burns, J.M.Paterson, J.D.Martin, J.P.Townsend, P.Waters, H.W.Clark, U.Kishore, K.B.Reid, T.J.Greenhough.

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.

Selected figure(s)

Figure 2.
Fig. 2. The manα1–2man-bound rfhSP-D trimer showing the bound manα1–2man (only the terminal mannose man1 is visible in the electron density) and the calcium ions (green spheres). (a) Viewed down the molecular 3-fold axis. (b) Viewed perpendicular to the molecular 3-fold axis.

Figure 3.
Fig. 3. The coordination of the calcium ion Ca1 and the bound ligands in selected subunits of the rfhSP-D–ligand complexes. (a) Chain B of the inositol phosphate structure. (b) Chain A, maltose. (c) Chain A, galactose. (d) Chain A, manα1–2man. (e) Chain B, manα1–4man. (f) Chain A, manα1–4man.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2009, 394, 776-788) copyright 2009.

Figures were selected by an automated process.