1prp
From Proteopedia
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|PDB= 1prp |SIZE=350|CAPTION= <scene name='initialview01'>1prp</scene>, resolution 2.100Å | |PDB= 1prp |SIZE=350|CAPTION= <scene name='initialview01'>1prp</scene>, resolution 2.100Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=TNT:1,3-BIS(AMIDINOPHENOXY)PROPANE'>TNT</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=TNT:1,3-BIS(AMIDINOPHENOXY)PROPANE'>TNT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1prp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1prp OCA], [http://www.ebi.ac.uk/pdbsum/1prp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1prp RCSB]</span> | ||
}} | }} | ||
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[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
[[Category: Nunn, C M.]] | [[Category: Nunn, C M.]] | ||
| - | [[Category: TNT]] | ||
[[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 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:03:41 2008'' |
Revision as of 20:03, 30 March 2008
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| , resolution 2.100Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF D(CGCGAATTCGCG) COMPLEXED WITH PROPAMIDINE, A SHORT-CHAIN HOMOLOGUE OF THE DRUG PENTAMIDIN
Overview
The crystal structure of the complex between propamidine and the self-complementary DNA dodecamer d(CGCGAATTCGCG) duplex has been determined to a resolution of 2.1 A and a R-factor of 17.4%. The propamidine binds to the DNA within the minor groove, with specific hydrogen-bonding interactions from the amidinium groups to the bases and sugar groups of the DNA, via a 4-base-pair binding site. A network of water molecules lies over the mouth of the minor groove. The structure provides a rationale for the superior DNA-binding properties of propamidine as compared to pentamidine [cf. Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. This is seen to result from (i) decreased minor groove width at the binding site and (ii) reduced mobility of the bound propamidine molecule.
About this Structure
1PRP is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine., Nunn CM, Jenkins TC, Neidle S, Biochemistry. 1993 Dec 21;32(50):13838-43. PMID:8268158
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