6ddg: Difference between revisions

<table><tr><td colspan='2'>[[6ddg]] is a 27 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DDG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DDG FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G6M:2-chloro-N-({(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide'>G6M</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ddd|6ddd]]</td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ddg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ddg OCA], [http://pdbe.org/6ddg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ddg RCSB], [http://www.ebi.ac.uk/pdbsum/6ddg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ddg ProSAT]</span></td></tr>

[[http://www.uniprot.org/uniprot/A0A077UUA0_STAAU A0A077UUA0_STAAU]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/W8TRD5_STAAU W8TRD5_STAAU]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326]  One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/B3VKN3_STAAU B3VKN3_STAAU]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/A0A077UGA7_STAAU A0A077UGA7_STAAU]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00687840] [[http://www.uniprot.org/uniprot/A0A077UVB6_STAAU A0A077UVB6_STAAU]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/A0A077V4G0_STAAU A0A077V4G0_STAAU]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342][RuleBase:RU004414] [[http://www.uniprot.org/uniprot/W8TUB4_STAAU W8TUB4_STAAU]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/W8TRE0_STAAU W8TRE0_STAAU]] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/A0A077VMP6_STAAU A0A077VMP6_STAAU]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.[HAMAP-Rule:MF_00382][RuleBase:RU000560] [[http://www.uniprot.org/uniprot/W8U3W0_STAAU W8U3W0_STAAU]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325][RuleBase:RU003906] [[http://www.uniprot.org/uniprot/W8TUE6_STAAU W8TUE6_STAAU]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366][RuleBase:RU003878][SAAS:SAAS00725369] [[http://www.uniprot.org/uniprot/A0A133Q8Z9_STAAU A0A133Q8Z9_STAAU]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01334][SAAS:SAAS00720025] [[http://www.uniprot.org/uniprot/D7URR3_STAAU D7URR3_STAAU]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562] [[http://www.uniprot.org/uniprot/A0A166DK89_STAAU A0A166DK89_STAAU]] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328]  One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/A0A077UKF9_STAAU A0A077UKF9_STAAU]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.[HAMAP-Rule:MF_01331]  This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g., L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331][RuleBase:RU004008]

[[Category: Bamert, R S]]

[[Category: Belousoff, M J]]

[[Category: Lithgow, T]]

[[Category: Venugopal, H]]

[[Category: Ribosome-antibiotic complex]]