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| | ==Crystal structure of inositol phosphate bound trimeric human lung surfactant protein D== | | ==Crystal structure of inositol phosphate bound trimeric human lung surfactant protein D== |
| - | <StructureSection load='3ikp' size='340' side='right' caption='[[3ikp]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='3ikp' size='340' side='right'caption='[[3ikp]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ikp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IKP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ikp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKP FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IPD:D-MYO-INOSITOL-1-PHOSPHATE'>IPD</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pw9|1pw9]], [[1pwb|1pwb]], [[3ikn|3ikn]], [[3ikq|3ikq]], [[3ikr|3ikr]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=IPD:D-MYO-INOSITOL-1-PHOSPHATE'>IPD</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ikp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikp OCA], [https://pdbe.org/3ikp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikp RCSB], [https://www.ebi.ac.uk/pdbsum/3ikp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikp ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ikp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikp OCA], [http://pdbe.org/3ikp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ikp RCSB], [http://www.ebi.ac.uk/pdbsum/3ikp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikp ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties. | + | [https://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikp_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikp_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Greenhough, T J]] | + | [[Category: Large Structures]] |
| - | [[Category: Shrive, A K]] | + | [[Category: Greenhough TJ]] |
| - | [[Category: Collagen]] | + | [[Category: Shrive AK]] |
| - | [[Category: Disulfide bond]]
| + | |
| - | [[Category: Extracellular matrix]]
| + | |
| - | [[Category: Gaseous exchange]]
| + | |
| - | [[Category: Glycoprotein]]
| + | |
| - | [[Category: Hydroxylation]]
| + | |
| - | [[Category: Lectin]]
| + | |
| - | [[Category: Neck+crd]]
| + | |
| - | [[Category: Secreted]]
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| - | [[Category: Sugar binding protein]]
| + | |
| - | [[Category: Surface film]]
| + | |
| - | [[Category: Trimeric recombinant fragment]]
| + | |
| Structural highlights
Function
SFTPD_HUMAN Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325.,Shrive AK, Martin C, Burns I, Paterson JM, Martin JD, Townsend JP, Waters P, Clark HW, Kishore U, Reid KB, Greenhough TJ J Mol Biol. 2009 Dec 11;394(4):776-88. Epub 2009 Sep 30. PMID:19799916[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shrive AK, Martin C, Burns I, Paterson JM, Martin JD, Townsend JP, Waters P, Clark HW, Kishore U, Reid KB, Greenhough TJ. Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325. J Mol Biol. 2009 Dec 11;394(4):776-88. Epub 2009 Sep 30. PMID:19799916 doi:10.1016/j.jmb.2009.09.057
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