1cvy
From Proteopedia
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|PDB= 1cvy |SIZE=350|CAPTION= <scene name='initialview01'>1cvy</scene>, resolution 2.15Å | |PDB= 1cvy |SIZE=350|CAPTION= <scene name='initialview01'>1cvy</scene>, resolution 2.15Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=IPY:IMIDAZOLE-PYRROLE POLYAMIDE'>IPY</scene> | + | |LIGAND= <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=IPY:IMIDAZOLE-PYRROLE+POLYAMIDE'>IPY</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1cvx|1CVX]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvy OCA], [http://www.ebi.ac.uk/pdbsum/1cvy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cvy RCSB]</span> | ||
}} | }} | ||
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[[Category: Rees, D. C.]] | [[Category: Rees, D. C.]] | ||
[[Category: White, S.]] | [[Category: White, S.]] | ||
| - | [[Category: IPY]] | ||
[[Category: double drug in minor groove]] | [[Category: double drug in minor groove]] | ||
[[Category: imidazole-pyrrole polyamide]] | [[Category: imidazole-pyrrole polyamide]] | ||
[[Category: minor groove recognition]] | [[Category: minor groove recognition]] | ||
| - | ''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 19:29:35 2008'' |
Revision as of 16:29, 30 March 2008
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| , resolution 2.15Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Related: | 1CVX
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG
Overview
Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.
About this Structure
1CVY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove., Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC, J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:10623546
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