2buk
From Proteopedia
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|PDB= 2buk |SIZE=350|CAPTION= <scene name='initialview01'>2buk</scene>, resolution 2.45Å | |PDB= 2buk |SIZE=350|CAPTION= <scene name='initialview01'>2buk</scene>, resolution 2.45Å | ||
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2buk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2buk OCA], [http://www.ebi.ac.uk/pdbsum/2buk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2buk RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2BUK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2BUK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Tobacco_necrosis_satellite_virus_1 Tobacco necrosis satellite virus 1]. This structure supersedes the now removed PDB entry 2STV. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BUK OCA]. |
==Reference== | ==Reference== | ||
Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution., Jones TA, Liljas L, J Mol Biol. 1984 Aug 25;177(4):735-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6481804 6481804] | Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution., Jones TA, Liljas L, J Mol Biol. 1984 Aug 25;177(4):735-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6481804 6481804] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Tobacco necrosis satellite virus | + | [[Category: Tobacco necrosis satellite virus 1]] |
[[Category: Jones, T A.]] | [[Category: Jones, T A.]] | ||
[[Category: Liljas, L.]] | [[Category: Liljas, L.]] | ||
| - | + | [[Category: capsid,tobacco necrosis satellite virus,virus/viral protein]] | |
| - | [[Category: capsid]] | + | |
[[Category: icosahedral virus]] | [[Category: icosahedral virus]] | ||
| - | [[Category: tobacco necrosis satellite virus]] | ||
| - | [[Category: virus/viral protein]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:11:59 2008'' |
Revision as of 23:11, 30 March 2008
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| , resolution 2.45Å | |||||||
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| Sites: | |||||||
| Ligands: | |||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SATELLITE TOBACCO NECROSIS VIRUS
Overview
The structure of the protein subunit of satellite tobacco necrosis virus has been solved at 3.7 A resolution. We have now crystallographically refined the original model and extended the resolution ot 2.5 A in order to get a model accurate enough to explain the details of the subunit interactions. The refinement was done with a novel method utilizing the icosahedral symmetry of the virus particle. The final model shows a complicated network of interactions, involving salt linkages, hydrogen bonds and hydrophobic contacts. In addition, we have located three different metal ion sites in the protein shell, linking the protein subunits together. These sites are probably occupied by calcium ions. One site is found in a general position near the icosahedral 3-fold axis of the virus. The ligands form an octahedral arrangement, with two main chain carbonyl oxygens (0-61 and 0-64), one carboxylate oxygen (OD1 from Asp194) of the same subunit and a second carboxylate oxygen (OE1 of Glu25) from a 3-fold related subunit. Two water molecules complete the octahedral arrangement. A second site is on the icosahedral 3-fold axis and is liganded by the carboxylate oxygens of the 3-fold related Asp55 residues. The third metal ion site is found on the 5-fold axis, liganded by the five carbonyl oxygens of Thr138 and two water molecules. We are unable to locate the first 11 N-terminal amino acid residues, which point into the virus interior. No interpretable density for RNA has been found, indicating that the nucleic acid of the virus does not have a unique orientation in the crystal.
About this Structure
2BUK is a Single protein structure of sequence from Tobacco necrosis satellite virus 1. This structure supersedes the now removed PDB entry 2STV. Full crystallographic information is available from OCA.
Reference
Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution., Jones TA, Liljas L, J Mol Biol. 1984 Aug 25;177(4):735-67. PMID:6481804
Page seeded by OCA on Mon Mar 31 02:11:59 2008
