This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1pfe

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:10, 3 April 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1pfe.gif|left|200px]]
 
-
{{Structure
+
==Echinomycin-(gcgtacgc)2 complex==
-
|PDB= 1pfe |SIZE=350|CAPTION= <scene name='initialview01'>1pfe</scene>, resolution 1.10&Aring;
+
<StructureSection load='1pfe' size='340' side='right'caption='[[1pfe]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=NCY:N-METHYLCYSTEINE'>NCY</scene>, <scene name='pdbligand=QUI:2-CARBOXYQUINOXALINE'>QUI</scene>, <scene name='pdbligand=SER:SERINE'>SER</scene>
+
<table><tr><td colspan='2'>[[1pfe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_echinatus Streptomyces echinatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PFE FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=N2C:N,S-DIMETHYLCYSTEINE'>N2C</scene>, <scene name='pdbligand=NCY:N-METHYLCYSTEINE'>NCY</scene>, <scene name='pdbligand=QUI:2-CARBOXYQUINOXALINE'>QUI</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=1pfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pfe OCA], [https://pdbe.org/1pfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pfe RCSB], [https://www.ebi.ac.uk/pdbsum/1pfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pfe ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pfe OCA], [http://www.ebi.ac.uk/pdbsum/1pfe PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pfe RCSB]</span>
+
__TOC__
-
}}
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
'''Echinomycin-(gcgtacgc)2 complex'''
+
[[Category: Streptomyces echinatus]]
-
 
+
[[Category: Cuesta-Seijo JA]]
-
 
+
-
==Overview==
+
-
The structure of the bis-intercalation complex of the depsipeptide antibiotic echinomycin with (CGTACG)2 has been redetermined at a higher resolution (1.4 A) and new high-resolution structures (1.1-1.5 A) are reported for the complexes of echinomycin with (GCGTACGC)2 (at both low and high ionic strengths) and (ACGTACGT)2. The structures show the expected Hoogsteen pairing for the base pairs flanking the intercalating chromophores on the outside and Watson-Crick pairing for both base pairs enclosed by the echinomycin. In the octamer complexes but not the hexamer complex, the echinomycin molecule, which would possess a molecular twofold axis were it not for the thioacetal bridge, shows twofold disorder. In all the structures the stacking of the base pairs and chromophores is extended by intermolecular stacking. The structures provide more precise details of the hydrogen bonding and other interactions between the bis-intercalating antibiotics and the duplex DNA than were previously available.
+
-
 
+
-
==About this Structure==
+
-
1PFE is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PFE OCA].
+
-
 
+
-
==Reference==
+
-
Structures of complexes between echinomycin and duplex DNA., Cuesta-Seijo JA, Sheldrick GM, Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):442-8. Epub 2005, Mar 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15805599 15805599]
+
-
[[Category: Protein complex]]
+
-
[[Category: Cuesta-Seijo, J A.]]
+
-
[[Category: bisintercalator]]
+
-
[[Category: duplex dna]]
+
-
[[Category: echinomycin]]
+
-
[[Category: hoogsteen base pairing]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:58:52 2008''
+

Current revision

Echinomycin-(gcgtacgc)2 complex

PDB ID 1pfe

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pfe"
Personal tools