1Z8V

The Structure of d(GGCCAATTGG) Complexed with Netropsin

Summary for 1Z8V

• Entry DOI: 10.2210/pdb1z8v/pdb
• Descriptor: (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'), NETROPSIN (3 entities in total)
• Functional Keywords: b-dna double helix, base triplets, minor groove binder, drug, netropsin, dna
• Total number of polymer chains: 2
• Total formula weight: 6600.52

Authors

Van Hecke, K.,Nam, P.C.,Nguyen, M.T.,Van Meervelt, L. (deposition date: 2005-03-31, release date: 2006-03-14, Last modification date: 2024-04-03)

Primary citation

Van Hecke, K.,Nam, P.C.,Nguyen, M.T.,Van Meervelt, L.
Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations.
Febs J., 272:3531-3541, 2005

PubMed Abstract: The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using refmac5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 A, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.

PubMed: 16008554
DOI: 10.1111/j.1742-4658.2005.04773.x

Experimental method

X-RAY DIFFRACTION (1.75 Å)