2rb2: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2rb2.jpg|left|200px]]


{{Structure
==3-methylbenzylazide in complex with T4 lysozyme L99A==
|PDB= 2rb2 |SIZE=350|CAPTION= <scene name='initialview01'>2rb2</scene>, resolution 1.463&Aring;
<StructureSection load='2rb2' size='340' side='right'caption='[[2rb2]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Po4+Binding+Site+For+Residue+X+2001'>AC1</scene>, <scene name='pdbsite=AC2:Po4+Binding+Site+For+Residue+X+2002'>AC2</scene>, <scene name='pdbsite=AC3:Po4+Binding+Site+For+Residue+X+2003'>AC3</scene> and <scene name='pdbsite=AC4:263+Binding+Site+For+Residue+X+1001'>AC4</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
<table><tr><td colspan='2'>[[2rb2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RB2 FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.463&#8491;</td></tr>
|GENE= E ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=263:1-(AZIDOMETHYL)-3-METHYLBENZENE'>263</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [https://pdbe.org/2rb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rb2 ProSAT]</span></td></tr>
|RELATEDENTRY=[[181l|181L]], [[1lgu|1LGU]], [[2ray|2RAY]], [[2raz|2RAZ]], [[2rb0|2RB0]], [[2rb1|2RB1]], [[2rbn|2RBN]], [[2rbo|2RBO]], [[2rbp|2RBP]], [[2rbq|2RBQ]], [[2rbr|2RBR]], [[2ras|2RAS]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rb2 OCA], [http://www.ebi.ac.uk/pdbsum/2rb2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2rb2 RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
== 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/rb/2rb2_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2rb2 ConSurf].
<div style="clear:both"></div>


'''3-methylbenzylazide in complex with T4 lysozyme L99A'''
==See Also==
 
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
 
== References ==
==Overview==
<references/>
Molecular docking computationally screens thousands to millions of organic molecules against protein structures, looking for those with complementary fits. Many approximations are made, often resulting in low "hit rates." A strategy to overcome these approximations is to rescore top-ranked docked molecules using a better but slower method. One such is afforded by molecular mechanics-generalized Born surface area (MM-GBSA) techniques. These more physically realistic methods have improved models for solvation and electrostatic interactions and conformational change compared to most docking programs. To investigate MM-GBSA rescoring, we re-ranked docking hit lists in three small buried sites: a hydrophobic cavity that binds apolar ligands, a slightly polar cavity that binds aryl and hydrogen-bonding ligands, and an anionic cavity that binds cationic ligands. These sites are simple; consequently, incorrect predictions can be attributed to particular errors in the method, and many likely ligands may actually be tested. In retrospective calculations, MM-GBSA techniques with binding-site minimization better distinguished the known ligands for each cavity from the known decoys compared to the docking calculation alone. This encouraged us to test rescoring prospectively on molecules that ranked poorly by docking but that ranked well when rescored by MM-GBSA. A total of 33 molecules highly ranked by MM-GBSA for the three cavities were tested experimentally. Of these, 23 were observed to bind--these are docking false negatives rescued by rescoring. The 10 remaining molecules are true negatives by docking and false positives by MM-GBSA. X-ray crystal structures were determined for 21 of these 23 molecules. In many cases, the geometry prediction by MM-GBSA improved the initial docking pose and more closely resembled the crystallographic result; yet in several cases, the rescored geometry failed to capture large conformational changes in the protein. Intriguingly, rescoring not only rescued docking false positives, but also introduced several new false positives into the top-ranking molecules. We consider the origins of the successes and failures in MM-GBSA rescoring in these model cavity sites and the prospects for rescoring in biologically relevant targets.
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Escherichia virus T4]]
2RB2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RB2 OCA].
[[Category: Large Structures]]
 
[[Category: Boyce SE]]
==Reference==
[[Category: Graves AP]]
Rescoring docking hit lists for model cavity sites: predictions and experimental testing., Graves AP, Shivakumar DM, Boyce SE, Jacobson MP, Case DA, Shoichet BK, J Mol Biol. 2008 Mar 28;377(3):914-34. Epub 2008 Jan 30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18280498 18280498]
[[Category: Shoichet BK]]
[[Category: Enterobacteria phage t4]]
[[Category: Lysozyme]]
[[Category: Single protein]]
[[Category: Boyce, S E.]]
[[Category: Graves, A P.]]
[[Category: Shoichet, B K.]]
[[Category: hydrolase]]
[[Category: protein cavity]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:58:29 2008''

Latest revision as of 12:21, 21 February 2024

3-methylbenzylazide in complex with T4 lysozyme L99A3-methylbenzylazide in complex with T4 lysozyme L99A

Structural highlights

2rb2 is a 1 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.463Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENLYS_BPT4 Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.[1]

Evolutionary Conservation

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

See Also

References

  1. ↑ Moussa SH, Kuznetsov V, Tran TA, Sacchettini JC, Young R. Protein determinants of phage T4 lysis inhibition. Protein Sci. 2012 Apr;21(4):571-82. doi: 10.1002/pro.2042. Epub 2012 Mar 2. PMID:22389108 doi:http://dx.doi.org/10.1002/pro.2042

2rb2, resolution 1.46Å

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=2rb2&oldid=4063121"