1unm: Difference between revisions

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-{{Seed}}
-[[Image:1unm.png|left|200px]]
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+==Crystal structure of 7-Aminoactinomycin D with non-complementary DNA==
-The line below this paragraph, containing "STRUCTURE_1unm", creates the "Structure Box" on the page.
+<StructureSection load='1unm' size='340' side='right'caption='[[1unm]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1unm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UNM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UNM FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PX1:(1Z)-7-AMINO-1-(HYDROXYMETHYLENE)-2-IMINO-4,6-DIMETHYL-3-OXO-2,3-DIHYDRO-1H-PHENOXAZINE-9-CARBALDEHYDE'>PX1</scene>, <scene name='pdbligand=SAR:SARCOSINE'>SAR</scene></td></tr>
-{{STRUCTURE_1unm|  PDB=1unm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1unm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1unm OCA], [https://pdbe.org/1unm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1unm RCSB], [https://www.ebi.ac.uk/pdbsum/1unm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1unm ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution and by molecular modelling. The crystal structures of the complex with 5'-TTAG[Br(5)U]T-3' provide interesting examples of MAD phasing in which the dispersive component of the MAD signal was almost certainly enhanced by radiation damage. The trigonal and orthorhombic crystal modifications both contain antibiotic molecules and DNA strands in the form of a 2:4 complex: in the orthorhombic form there is one such complex in the asymmetric unit, while in the trigonal structure there are four. In both structures the phenoxazone ring of the first drug intercalates between a BrU-G (analogous to T-G) wobble pair and a G-T pair where the T is part of a symmetry-related molecule. The chromophore of the second actinomycin intercalates between the BrU-G and G-BrU wobble pairs of the partially paired third and fourth strands. The base stacking also involves (A*T)*T triplets and Watson-Crick A-T pairs and leads to similar complex three-dimensional networks in both structures, with looping-out of unpaired bases. Although the available NOE constraints of a solution containing the antibiotic and d(TTTAGTTT) strands in the ratio 1:1 are insufficient to determine the structure of the complex from the NMR data alone, they are consistent with the intercalation geometry observed in the crystal structure. Molecular-dynamics (MD) trajectories starting from the 1:2 complexes observed in the crystal showed that although the thymines flanking the d(AGT) core are rather flexible and the G-T pairing is not permanently preserved, both strands remain bound to the actinomycin by strong interactions between it and the guanines between which it is sandwiched. Similar strong binding (hemi-intercalation) of the actinomycin to a single guanine was observed in the MD trajectories of a 1:1 complex. The dominant interaction is between the antibiotic and guanine, but the complexes are stabilized further by promiscuous base-pairing.
-===CRYSTAL STRUCTURE OF 7-AMINOACTINOMYCIN D WITH NON-COMPLEMENTARY DNA===
+Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT).,Alexopoulos E, Jares-Erijman EA, Jovin TM, Klement R, Machinek R, Sheldrick GM, Uson I Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):407-15. Epub 2005, Mar 24. PMID:15805595<ref>PMID:15805595</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15805595}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1unm" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15805595 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15805595}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-UNM is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UNM OCA].
+[[Category: Streptomyces antibioticus]]
+[[Category: Synthetic construct]]
-==Reference==
+[[Category: Alexopoulos EC]]
-Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)., Alexopoulos E, Jares-Erijman EA, Jovin TM, Klement R, Machinek R, Sheldrick GM, Uson I, Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):407-15. Epub 2005, Mar 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15805595 15805595]
+[[Category: Jares-Erijman EA]]
-[[Category: Single protein]]
+[[Category: Jovin TM]]
-[[Category: Alexopoulos, E C.]]
+[[Category: Klement R]]
-[[Category: Jares-Erijman, E A.]]
+[[Category: Sheldrick GM]]
-[[Category: Jovin, T M.]]
+[[Category: Uson I]]
-[[Category: Klement, R.]]
-[[Category: Sheldrick, G M.]]
-[[Category: Uson, I.]]
-[[Category: Actinomycin d]]
-[[Category: Intercalator]]
-[[Category: Non-complementary dna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 13:10:23 2008''