1gyk
From Proteopedia
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|PDB= 1gyk |SIZE=350|CAPTION= <scene name='initialview01'>1gyk</scene>, resolution 2.2Å | |PDB= 1gyk |SIZE=350|CAPTION= <scene name='initialview01'>1gyk</scene>, resolution 2.2Å | ||
|SITE= <scene name='pdbsite=CA1:Ca+Binding+Site+For+Chain+E'>CA1</scene> | |SITE= <scene name='pdbsite=CA1:Ca+Binding+Site+For+Chain+E'>CA1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CDG:METHYL+4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE'>CDG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<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://www.ebi.ac.uk/pdbsum/1gyk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1gyk RCSB]</span> | ||
}} | }} | ||
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==Overview== | ==Overview== | ||
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. | 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. | ||
| - | |||
| - | ==Disease== | ||
| - | Known disease associated with this structure: Amyloidosis, secondary, susceptibility to OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=104770 104770]] | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Tickle, I.]] | [[Category: Tickle, I.]] | ||
[[Category: Wood, S P.]] | [[Category: Wood, S P.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: CDG]] | ||
[[Category: amyloid lectin]] | [[Category: amyloid lectin]] | ||
[[Category: glycoprotein]] | [[Category: glycoprotein]] | ||
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[[Category: polymorphism]] | [[Category: polymorphism]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:53:59 2008'' |
Revision as of 17:54, 30 March 2008
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| , resolution 2.2Å | |||||||
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| Sites: | |||||||
| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SERUM AMYLOID P COMPONENT CO-CRYSTALLISED WITH MOBDG AT NEUTRAL PH
Overview
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.
About this Structure
1GYK is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
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
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