1d64: Difference between revisions

Revision as of 13:29, 2 May 2008

CRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLICATIONS FOR DNA-BINDING PROPERTIES

OverviewOverview

The crystal structure of the complex formed between the dodecanucleotide d(CGCGAATTCGCG)2 and the drug pentamidine, which is active against the Pneumocystis carinii pathogen in AIDS patients, has been determined to a resolution of 2.1 A and an R-factor of 19.4%. Analysis of the structure has shown the drug to be bound in the 5'-AATT minor groove region of the duplex, with the amidinium groups H-bonded to adenine N3 atoms in an interstrand manner. The drug molecule adopts an extended conformation, and the immediate binding site spans four base pairs. Structural details of the drug-DNA interactions are discussed, and comparison is made with the dodecamer complex of the structurally similar berenil ligand.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties., Edwards KJ, Jenkins TC, Neidle S, Biochemistry. 1992 Aug 11;31(31):7104-9. PMID:1643044 Page seeded by OCA on Fri May 2 13:29:36 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:1d64.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1d64 |SIZE=350|CAPTION= <scene name='initialview01'>1d64</scene>, resolution 2.100&Aring;
+The line below this paragraph, containing "STRUCTURE_1d64", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <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=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=PNT:1,3-BIS(4-AMIDINOPHENOXY)PENTANE'>PNT</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1d64|  PDB=1d64  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d64 OCA], [http://www.ebi.ac.uk/pdbsum/1d64 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d64 RCSB]</span>
-}}
 '''CRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLICATIONS FOR DNA-BINDING PROPERTIES'''
@@ Line 19: / Line 16: @@
 ==About this Structure==
-D64 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=1D64 OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D64 OCA].
 ==Reference==
 Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties., Edwards KJ, Jenkins TC, Neidle S, Biochemistry. 1992 Aug 11;31(31):7104-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1643044 1643044]
-[[Category: Protein complex]]
 [[Category: Edwards, K J.]]
 [[Category: Jenkins, T C.]]
 [[Category: Neidle, S.]]
-[[Category: b-dna]]
+[[Category: B-dna]]
-[[Category: complexed with drug]]
+[[Category: Complexed with drug]]
-[[Category: double helix]]
+[[Category: Double helix]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:29:36 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:35:28 2008''