1dvl
From Proteopedia
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CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END
Overview
The crystal structure of the 1:1 complex of netropsin and the B-DNA, decamer d(CCIICICCII)(2) has been elucidated and refined to an R factor of, 19.6% and an R(free) of 24.7% using 1790 reflections in the resolution, range 8-2.4 A. The complex crystallizes in space group C2, with unit-cell, parameters a = 62.40, b = 24.47, c = 36.31 A, beta = 110.09 degrees and, one molecule of netropsin in the asymmetric unit; the rest of the minor, groove is filled with six water molecules. The structure was solved by the, molecular-replacement method using the DNA model d(CCCCCIIIII)(2) from the, 2:1 netropsin complex by removing both bound netropsins (Chen et al., 1998). Surprisingly, only one netropsin molecule is found to bind to the, present decamer, covering residues 2-6 at the upper stream of the duplex., The positively charged guanidinium head is hydrogen bonded through N1H(2), to the O(2) of cytosine 2 and through N10H(2) to N(3) of inosine 6. The, three amide N-H groups of the peptides face the minor groove and form, three sets of bifurcated hydrogen bonds with the base atoms. The central, part of the drug (C3-N8) is nearly conjugated. The preference of the, cytosine carbonyl O2 atoms over the inosine N3 atoms in hydrogen bonding, is seen. The drug-bound region has more uniform twists, roll angles, propeller twists and minor-groove widths compared with the water-bound, region.
About this Structure
1DVL is a Protein complex structure of sequences from [1] with NT as ligand. Full crystallographic information is available from OCA.
Reference
Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin., Shi K, Mitra SN, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):601-6. Epub 2002, Mar 22. PMID:11914483
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