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1gyk

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Revision as of 06:45, 3 January 2018

Serum Amyloid P Component co-crystallised with MOBDG at neutral pH

Structural highlights

1gyk 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.
Ligands:	,
Related:	1lgn, 1sac
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

Two monoclinic (P2(1)) crystal forms of human serum amyloid P component (SAP) in complex with the 4,6-pyruvate acetal of beta-D-galactose (MObetaDG) were prepared. Structure analysis by molecular replacement and refinement at 2.2A resolution revealed that crystal form 1 (a=95.76A, b=70.53A, c=103.41A, beta=96.80 degrees) contained a pentamer in the asymmetric unit with a structure very similar to that of the published search model. The mode of ligand co-ordination was also similar except that four of the five subunits showed bound ligand with an additional H-bond between O1 of the galactose and the side-chain of Lys79. One sub-unit showed no bound ligand and a vacant calcium site close to a crystal contact. The 2.6A resolution structure of crystal form 2 (a=118.60A, b=109.10A, c=120.80A and beta=95.16 degrees ) showed ten sub-units in the asymmetric unit, all with two bound calcium ions and ligand. The most extensive protein-protein interactions between pentamers describe an AB face-to-face interaction involving 15 ion pairs that sandwiches five molecules of bound MObetaDG at the interface.

The structures of crystalline complexes of human serum amyloid P component with its carbohydrate ligand, the cyclic pyruvate acetal of galactose.,Thompson D, Pepys MB, Tickle I, Wood S J Mol Biol. 2002 Jul 26;320(5):1081-6. PMID:12126626^[1]

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

References

↑ Thompson D, Pepys MB, Tickle I, Wood S. The structures of crystalline complexes of human serum amyloid P component with its carbohydrate ligand, the cyclic pyruvate acetal of galactose. J Mol Biol. 2002 Jul 26;320(5):1081-6. PMID:12126626

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
-==SERUM AMYLOID P COMPONENT CO-CRYSTALLISED WITH MOBDG AT NEUTRAL PH==
+==Serum Amyloid P Component co-crystallised with MOBDG at neutral pH==
 <StructureSection load='1gyk' size='340' side='right' caption='[[1gyk]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
@@ Line 5: / Line 6: @@
 </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=CDG:METHYL+4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE'>CDG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lgn|1lgn]], [[1sac|1sac]]</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=1gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyk OCA], [http://pdbe.org/1gyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyk RCSB], [http://www.ebi.ac.uk/pdbsum/1gyk PDBsum]</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=1gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyk OCA], [http://pdbe.org/1gyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gyk RCSB], [http://www.ebi.ac.uk/pdbsum/1gyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyk ProSAT]</span></td></tr>
 </table>
 == Disease ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/1gyk_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gy/1gyk_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 43: / Line 44: @@
 [[Category: Pentraxin]]
 [[Category: Plasma]]
+[[Category: Polymorphism]]

1gyk

From Proteopedia

Revision as of 06:45, 3 January 2018

Serum Amyloid P Component co-crystallised with MOBDG at neutral pH

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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