1ddl
From Proteopedia
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|PDB= 1ddl |SIZE=350|CAPTION= <scene name='initialview01'>1ddl</scene>, resolution 2.7Å | |PDB= 1ddl |SIZE=350|CAPTION= <scene name='initialview01'>1ddl</scene>, resolution 2.7Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ddl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ddl OCA], [http://www.ebi.ac.uk/pdbsum/1ddl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ddl RCSB]</span> | ||
}} | }} | ||
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[[Category: water structure]] | [[Category: water structure]] | ||
| - | ''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 19:39:31 2008'' |
Revision as of 16:39, 30 March 2008
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| , resolution 2.7Å | |||||||
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| Ligands: | |||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
DESMODIUM YELLOW MOTTLE TYMOVIRUS
Overview
Desmodium yellow mottle virus is a 28 nm diameter, T=3 icosahedral plant virus of the tymovirus group. Its structure has been solved to a resolution of 2.7 A using X-ray diffraction analysis based on molecular replacement and phase extension methods. The final R value was 0.151 (R(free)=0.159) for 134,454 independent reflections. The folding of the polypeptide backbone is nearly identical with that of turnip yellow mosaic virus, as is the arrangement of subunits in the virus capsid. However, a major difference in the disposition of the amino-terminal ends of the subunits was observed. In turnip yellow mosaic virus, those from the B and C subunits comprising the hexameric capsomeres formed an annulus about the interior of the capsomere, while the corresponding N termini of the pentameric capsomere A subunits were not visible at all in electron density maps. In Desmodium yellow mottle tymovirus, amino termini from the A and B subunits combine to form the annuli, thereby resulting in a much strengthened association between the two types of capsomeres and an, apparently, more stable capsid. The first 13 residues of the C subunit were invisible in electron density maps. Two ordered fragments of single-stranded RNA, seven and two nucleotides in length, were observed. The ordered water structure of the virus particle was delineated and required 95 solvent molecules per protein subunit.
About this Structure
1DDL is a Single protein structure of sequence from Desmodium yellow mottle virus. Full crystallographic information is available from OCA.
Reference
Refined structure of desmodium yellow mottle tymovirus at 2.7 A resolution., Larson SB, Day J, Canady MA, Greenwood A, McPherson A, J Mol Biol. 2000 Aug 18;301(3):625-42. PMID:10966774
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