1akp: Difference between revisions

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-{{Seed}}
-[[Image:1akp.png|left|200px]]
-<!--
+==SEQUENTIAL 1H,13C AND 15N NMR ASSIGNMENTS AND SOLUTION CONFORMATION OF APOKEDARCIDIN==
-The line below this paragraph, containing "STRUCTURE_1akp", creates the "Structure Box" on the page.
+<StructureSection load='1akp' size='340' side='right'caption='[[1akp]]' 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'>[[1akp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomycete_ATCC_53650 Actinomycete ATCC 53650]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AKP 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">Solution NMR, 15 models</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=1akp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1akp OCA], [https://pdbe.org/1akp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1akp RCSB], [https://www.ebi.ac.uk/pdbsum/1akp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1akp ProSAT]</span></td></tr>
-{{STRUCTURE_1akp|  PDB=1akp  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KEDA_ACTSL KEDA_ACTSL] Binds non-covalently to an enediyne chromophore which is the cytotoxic and mutagenic component of the antibiotic. The chromophore cleaves duplex DNA site-specifically in a single-stranded manner. The apoprotein cleaves proteins selectively, in particular highly basic histones, with H1 proteins being cleaved the more readily.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Kedarcidin is a recently discovered antitumor antibiotic chromoprotein. The solution conformation of the kedarcidin apoprotein (114 residues) has been characterized by heteronuclear multidimensional NMR spectroscopy. Sequence-specific backbone atom resonance assignments were obtained for a uniformly 13C/15N-enriched sample of apokedarcidin via a semiautomated analysis of 3D HNCACB, 3D CBCA-(CO)NH, 4D HNCAHA, 4D HN(CO)CAHA, 3D HBHA(CO)NH, and 3D HNHA(Gly) spectra. Side-chain assignments were subsequently obtained by analysis of (primarily) 3D HCCH-TOCSY and HCCH-COSY spectra. A qualitative analysis of the secondary structure is presented on the basis of 3J alpha NH coupling constants, deviations of 13C alpha and 13C beta chemical shifts from random coil values, and NOEs observed in 3D 15N- and 13C-edited NOESY-HSQC spectra. This analysis revealed a four-stranded antiparallel beta-sheet, a three-stranded antiparallel beta-sheet, and two two-standed antiparallel beta-sheets. The assignments of cross-peaks in the 3D NOESY spectra were assisted by reference to a preliminary model of apokedarcidin built using the program CONGEN starting from the X-ray structure of the homologous protein aponeocarzinostatin. An ensemble of 15 apokedarcidin solution structures has been generated by variable target function minimization (DIANA program) and refined by simulated annealing (X-PLOR program). The average backbone atom root-mean-square difference between the individual structures and the mean coordinates is 0.68 +/- 0.08 A. The overall fold of apokedarcidin is well-defined; it is composed of an immunoglobulin-like seven-stranded antiparallel beta-barrel and a subdomain containing two antiparallel beta-ribbons. Highly similar tertiary structures have been previously reported for the related proteins neocarzinostatin, macromomycin, and actinoxanthin. Important structural features are revealed, including the dimensions of the chromophore-binding pocket and the locations of side chains that are likely to be involved in chromophore stabilization.
-===SEQUENTIAL 1H,13C AND 15N NMR ASSIGNMENTS AND SOLUTION CONFORMATION OF APOKEDARCIDIN===
+Sequential 1H, 13C, and 15N NMR assignments and solution conformation of apokedarcidin.,Constantine KL, Colson KL, Wittekind M, Friedrichs MS, Zein N, Tuttle J, Langley DR, Leet JE, Schroeder DR, Lam KS, et al. Biochemistry. 1994 Sep 27;33(38):11438-52. PMID:7918358<ref>PMID:7918358</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_7918358}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1akp" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 7918358 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_7918358}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Actinomycete ATCC 53650]]
-AKP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Actinomycete_sp9440 Actinomycete sp9440]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKP OCA].
+[[Category: Large Structures]]
+[[Category: Bruccoleri RE]]
-==Reference==
+[[Category: Colson KL]]
-Sequential 1H, 13C, and 15N NMR assignments and solution conformation of apokedarcidin., Constantine KL, Colson KL, Wittekind M, Friedrichs MS, Zein N, Tuttle J, Langley DR, Leet JE, Schroeder DR, Lam KS, et al., Biochemistry. 1994 Sep 27;33(38):11438-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7918358 7918358]
+[[Category: Constantine KL]]
-[[Category: Actinomycete sp9440]]
+[[Category: Farmer II BT]]
-[[Category: Single protein]]
+[[Category: Friedrichs MS]]
-[[Category: Bruccoleri, R E.]]
+[[Category: Lam KS]]
-[[Category: Colson, K L.]]
+[[Category: Langley DR]]
-[[Category: Constantine, K L.]]
+[[Category: Leet JE]]
-[[Category: Friedrichs, M S.]]
+[[Category: Metzler WJ]]
-[[Category: II, B T.Farmer.]]
+[[Category: Mueller L]]
-[[Category: Lam, K S.]]
+[[Category: Schroeder DR]]
-[[Category: Langley, D R.]]
+[[Category: Tuttle J]]
-[[Category: Leet, J E.]]
+[[Category: Wittekind M]]
-[[Category: Metzler, W J.]]
+[[Category: Zein N]]
-[[Category: Mueller, L.]]
-[[Category: Schroeder, D R.]]
-[[Category: Tuttle, J.]]
-[[Category: Wittekind, M.]]
-[[Category: Zein, N.]]
-[[Category: Antibiotic chromoprotein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 17:03:08 2008''