193d
From Proteopedia
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|PDB= 193d |SIZE=350|CAPTION= <scene name='initialview01'>193d</scene> | |PDB= 193d |SIZE=350|CAPTION= <scene name='initialview01'>193d</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CH3:METHYL+GROUP'>CH3</scene> | + | |LIGAND= <scene name='pdbligand=CH3:METHYL+GROUP'>CH3</scene>, <scene name='pdbligand=CPC:2-METHYL-1-METHYLAMINO-CYCLOPROPANE+CARBOXYLIC+ACID'>CPC</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=HQU:3-HYDROXYQUINALDIC+ACID'>HQU</scene>, <scene name='pdbligand=NBU:N-BUTANE'>NBU</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=193d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=193d OCA], [http://www.ebi.ac.uk/pdbsum/193d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=193d RCSB]</span> | ||
}} | }} | ||
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[[Category: Chen, H.]] | [[Category: Chen, H.]] | ||
[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
| - | [[Category: CH3]] | ||
| - | [[Category: NBU]] | ||
[[Category: dna]] | [[Category: dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
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[[Category: quinomycin]] | [[Category: quinomycin]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:29:58 2008'' |
Revision as of 15:30, 30 March 2008
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| Ligands: | , , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX
Overview
The quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical structure related to the antibiotic echinomycin which is known to bisintercalate into DNA. Common features among these antibiotics include two heterocyclic aromatic ring systems propagating from a cross-bridged cyclic octadepsipeptide scaffold. We report on the solution structure of the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex) based on a combined NMR-molecular dynamics study including intensity-based refinement. The 3-hydroxy quinaldic acid rings bisintercalate into the duplex at (A3-C4).(G5-T6) steps and stack with flanking Watson-Crick A3.T6 and C4.G5 base-pairs. The intercalation sites at (A3-C4).(G5-T6) steps are wedge-shaped and unwound, with significant unwinding also observed at the (C4-C5).(C4-G5) step bracketed between the intercalation sites. The cross-bridged cyclic octadepsipeptide is positioned in the minor groove with the methyl groups on its Ala and NMe-MCp residues directed towards and making van der Waals contacts with the minor groove edge of the duplex. A pair of adjacent intermolecular hydrogen bonds between the Ala backbone atoms and the G5 minor groove edge (Ala-NH to G5-N(3) and G5-NH2e to Ala-CO) account for the sequence specificity associated with complex formation. The solution structure of the QN-DNA oligomer complex, which contains only Watson-Crick base-pairs flanking the bisintercalation site, is compared with the crystal structure of the related echinomycin-DNA oligomer complex, which contains Hoogsteen base-pairs on either side of the bisintercalation site.
About this Structure
193D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of a quinomycin bisintercalator-DNA complex., Chen H, Patel DJ, J Mol Biol. 1995 Feb 10;246(1):164-79. PMID:7853395
Page seeded by OCA on Sun Mar 30 18:29:58 2008
Categories: Protein complex | Chen, H. | Patel, D J. | Dna | Double helix | Nmr | Quinomycin
