1lgn

From Proteopedia

(Difference between revisions)

Current revision

DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT

Structural highlights

1lgn is a 5 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

SAMP_HUMAN Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with amyloid deposits.

Function

SAMP_HUMAN Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.

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

Serum amyloid P component (SAP) is a glycoprotein that binds in a calcium-dependent fashion to a variety of ligands including other proteins, glycosaminoglycans and DNA. SAP is universally associated with the amyloid deposits in all forms of amyloidoses including Alzheimer's disease. Small-molecule ligands that displace SAP from amyloid fibrils and thereby expose the fibrils to proteolytic clearance mechanisms hold potential as drugs for the prevention and treatment of amyloidosis. We have carried out a screen for novel SAP ligands and have identified 2'-deoxyadenosine-5'-monophosphate (dAMP) as a ligand. The crystal structure of the SAP-dAMP complex determined at 2.8 A resolution (R = 0.232, R(free) = 0.252) reveals a decamer in which all interactions between SAP pentamers are mediated by the ligand. The stability of the decamer in solution has been demonstrated by gel filtration chromatography. The two calcium ions of SAP are bridged by the dAMP phosphate group and five hydrogen bonds are formed between the protein and the ligand, including specific interactions made by the adenine base. This mode of dAMP binding is not compatible with the nucleotide being part of double-helical DNA. The SAP-dAMP decamer is stabilized mainly by base-stacking of adjacent ligand molecules and possibly by electrostatic interactions involving the dAMP phosphate groups; decamerization buries 1000 A2 (2.6%) of the pentamer solvent-accessible surface. Ligand-induced decamerization of SAP, which utilizes the high cooperativity of a multiple-site interaction, may be a strategy to overcome the problems for drug design associated with the rather modest affinities of SAP for small-molecule ligands.

Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP.,Hohenester E, Hutchinson WL, Pepys MB, Wood SP J Mol Biol. 1997 Jun 20;269(4):570-8. PMID:9217261^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hohenester E, Hutchinson WL, Pepys MB, Wood SP. Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP. J Mol Biol. 1997 Jun 20;269(4):570-8. PMID:9217261 doi:10.1006/jmbi.1997.1075

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 See Also
7 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1lgn"

Categories: Homo sapiens | Large Structures | Hohenester E | Pepys MB | Wood SP

@@ Line 3: / Line 3: @@
 <StructureSection load='1lgn' size='340' side='right'caption='[[1lgn]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1lgn]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LGN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1lgn]] is a 5 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=1LGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LGN 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></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]] 2.8&#8491;</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=1lgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgn OCA], [http://pdbe.org/1lgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lgn RCSB], [http://www.ebi.ac.uk/pdbsum/1lgn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lgn ProSAT]</span></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=D5M:2-DEOXYADENOSINE-5-MONOPHOSPHATE'>D5M</scene></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=1lgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lgn OCA], [https://pdbe.org/1lgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lgn RCSB], [https://www.ebi.ac.uk/pdbsum/1lgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lgn ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/SAMP_HUMAN SAMP_HUMAN]] Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with amyloid deposits.
+[https://www.uniprot.org/uniprot/SAMP_HUMAN SAMP_HUMAN] Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with amyloid deposits.
 == Function ==
-[[http://www.uniprot.org/uniprot/SAMP_HUMAN SAMP_HUMAN]] Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.
+[https://www.uniprot.org/uniprot/SAMP_HUMAN SAMP_HUMAN] Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 17: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lg/1lgn_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>
   </jmolCheckbox>
@@ Line 30: / Line 31: @@
 </div>
 <div class="pdbe-citations 1lgn" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Serum amyloid P-component|Serum amyloid P-component]]
 == References ==
 <references/>
@@ Line 36: / Line 40: @@
 [[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Hohenester, E]]
+[[Category: Hohenester E]]
-[[Category: Pepys, M B]]
+[[Category: Pepys MB]]
-[[Category: Wood, S P]]
+[[Category: Wood SP]]
-[[Category: Amyloidosis]]
-[[Category: Drug design]]
-[[Category: Nucleotide]]
-[[Category: Serum protein]]

1lgn

From Proteopedia

Current revision

DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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