2f4v: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2f4v.png|left|200px]]


{{STRUCTURE_2f4v| PDB=2f4v | SCENE= }}  
==30S ribosome + designer antibiotic==
<StructureSection load='2f4v' size='340' side='right'caption='[[2f4v]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2f4v]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F4V FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AB9:(2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE'>AB9</scene>, <scene name='pdbligand=D2C:(2S,4S,4AR,5AS,6S,11R,11AS,12R,12AR)-7-CHLORO-4-(DIMETHYLAMINO)-6,10,11,12-TETRAHYDROXY-1,3-DIOXO-1,2,3,4,4A,5,5A,6,11,11A,12,12A-DODECAHYDROTETRACENE-2-CARBOXAMIDE'>D2C</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4v OCA], [https://pdbe.org/2f4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f4v RCSB], [https://www.ebi.ac.uk/pdbsum/2f4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f4v ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f4/2f4v_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f4v ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.


===30S ribosome + designer antibiotic===
Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site.,Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S Chem Biol. 2006 Feb;13(2):129-38. PMID:16492561<ref>PMID:16492561</ref>


{{ABSTRACT_PUBMED_16492561}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 2f4v" style="background-color:#fffaf0;"></div>
[[2f4v]] is a 21 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S14]], [[Ribosomal protein S15]], [[Ribosomal protein S16]], [[Ribosomal protein S17]], [[Ribosomal protein S18]], [[Ribosomal protein S19]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein S5]], [[Ribosomal protein S6]], [[Ribosomal protein S7]], [[Ribosomal protein S8]] and [[Ribosomal protein S9]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4V OCA].


==See Also==
==See Also==
*[[Ribosomal protein S10|Ribosomal protein S10]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Ribosomal protein S11|Ribosomal protein S11]]
== References ==
*[[Ribosomal protein S12|Ribosomal protein S12]]
<references/>
*[[Ribosomal protein S13|Ribosomal protein S13]]
__TOC__
*[[Ribosomal protein S14|Ribosomal protein S14]]
</StructureSection>
*[[Ribosomal protein S15|Ribosomal protein S15]]
[[Category: Large Structures]]
*[[Ribosomal protein S16|Ribosomal protein S16]]
*[[Ribosomal protein S17|Ribosomal protein S17]]
*[[Ribosomal protein S18|Ribosomal protein S18]]
*[[Ribosomal protein S19|Ribosomal protein S19]]
*[[Ribosomal protein S2|Ribosomal protein S2]]
*[[Ribosomal protein S20|Ribosomal protein S20]]
*[[Ribosomal protein S3|Ribosomal protein S3]]
*[[Ribosomal protein S4|Ribosomal protein S4]]
*[[Ribosomal protein S5|Ribosomal protein S5]]
*[[Ribosomal protein S6|Ribosomal protein S6]]
*[[Ribosomal protein S7|Ribosomal protein S7]]
*[[Ribosomal protein S8|Ribosomal protein S8]]
*[[Ribosomal protein S9|Ribosomal protein S9]]
 
==Reference==
<ref group="xtra">PMID:016492561</ref><references group="xtra"/>
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Haddad, J.]]
[[Category: Haddad J]]
[[Category: Lentzen, G.]]
[[Category: Lentzen G]]
[[Category: Meroueh, S O.]]
[[Category: Meroueh SO]]
[[Category: Mobashery, S.]]
[[Category: Mobashery S]]
[[Category: Murray, J B.]]
[[Category: Murray JB]]
[[Category: Russell, R J.]]
[[Category: Russell RJ]]
[[Category: 30s ribosome subunit]]
[[Category: Designer antibiotic]]
[[Category: Ribosome]]

Latest revision as of 08:12, 17 October 2024

30S ribosome + designer antibiotic30S ribosome + designer antibiotic

Structural highlights

2f4v is a 10 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.8Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS2_THET8 Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.

Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site.,Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S Chem Biol. 2006 Feb;13(2):129-38. PMID:16492561[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S. Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site. Chem Biol. 2006 Feb;13(2):129-38. PMID:16492561 doi:10.1016/j.chembiol.2005.11.004

2f4v, resolution 3.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2f4v&oldid=4191714"