6v3d: Difference between revisions

<table><tr><td colspan='2'>[[6v3d]] is a 29 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii], [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_(strain_ab0057) Acinetobacter baumannii (strain ab0057)], [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_ab0057 Acinetobacter baumannii ab0057], [http://en.wikipedia.org/wiki/Acinetobacter_beijerinckii_anc_3835 Acinetobacter beijerinckii anc 3835], [http://en.wikipedia.org/wiki/Acinetobacter_rudis_cip_110305 Acinetobacter rudis cip 110305], [http://en.wikipedia.org/wiki/Acinetobacter_sp._809848 Acinetobacter sp. 809848], [http://en.wikipedia.org/wiki/Acinetobacter_sp._anc_4470 Acinetobacter sp. anc 4470], [http://en.wikipedia.org/wiki/Acinetobacter_sp._cip_102082 Acinetobacter sp. cip 102082], [http://en.wikipedia.org/wiki/Acinetobacter_sp._cip_51.11 Acinetobacter sp. cip 51.11] and [http://en.wikipedia.org/wiki/Acinetobacter_sp._niph_899 Acinetobacter sp. niph 899]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V3D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V3D FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>

<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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=6v3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v3d OCA], [http://pdbe.org/6v3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v3d RCSB], [http://www.ebi.ac.uk/pdbsum/6v3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v3d ProSAT]</span></td></tr>

[[http://www.uniprot.org/uniprot/RL6_ACIB5 RL6_ACIB5]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. [[http://www.uniprot.org/uniprot/RL21_ACIB5 RL21_ACIB5]] This protein binds to 23S rRNA in the presence of protein L20. [[http://www.uniprot.org/uniprot/RL2_ACIB5 RL2_ACIB5]] 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. [[http://www.uniprot.org/uniprot/A0A009QSN8_9GAMM A0A009QSN8_9GAMM]] 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] [[http://www.uniprot.org/uniprot/RL18_ACIB5 RL18_ACIB5]] 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. [[http://www.uniprot.org/uniprot/RL23_ACIB5 RL23_ACIB5]] 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. [[http://www.uniprot.org/uniprot/RL13_ACIB5 RL13_ACIB5]] 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. [[http://www.uniprot.org/uniprot/RL16_ACIB5 RL16_ACIB5]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [[http://www.uniprot.org/uniprot/RL25_ACIB5 RL25_ACIB5]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. [[http://www.uniprot.org/uniprot/RL4_ACIB5 RL4_ACIB5]] 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.  Forms part of the polypeptide exit tunnel. [[http://www.uniprot.org/uniprot/RL9_ACIB5 RL9_ACIB5]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/N8WQT6_9GAMM N8WQT6_9GAMM]] 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/RL15_ACIB5 RL15_ACIB5]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/V5VGC9_ACIBA V5VGC9_ACIBA]] 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/RL3_ACIB5 RL3_ACIB5]] 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. [[http://www.uniprot.org/uniprot/RL24_ACIB5 RL24_ACIB5]] 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.  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RL5_ACIB5 RL5_ACIB5]] This is 1 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. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. [[http://www.uniprot.org/uniprot/RL19_ACIB5 RL19_ACIB5]] 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.

 

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== References ==

[[Category: Acinetobacter baumannii]]

[[Category: Acinetobacter beijerinckii anc 3835]]

[[Category: Acinetobacter rudis cip 110305]]

[[Category: Acinetobacter sp. 809848]]

[[Category: Acinetobacter sp. cip 102082]]

[[Category: Acinetobacter sp. cip 51 11]]

[[Category: Acinetobacter sp. niph 899]]

[[Category: Morgan, C E]]

[[Category: Yu, E W]]

[[Category: Ribosome]]