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PDBsum entry 198d
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Nucleic Acids Res
23:1710-1716
(1995)
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PubMed id:
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A trigonal form of the idarubicin:d(CGATCG) complex; crystal and molecular structure at 2.0 A resolution.
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A.Dautant,
B.Langlois d'Estaintot,
B.Gallois,
T.Brown,
W.N.Hunter.
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ABSTRACT
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The X-ray crystal structure of the complex between the anthracycline idarubicin
and d(CGATCG) has been solved by molecular replacement and refined to a
resolution of 2.0 A. The final R-factor is 0.19 for 3768 reflections with Fo
> or = 2 sigma (Fo). The complex crystallizes in the trigonal space group P31
with unit cell parameters a = b = 52.996(4), c = 33.065(2) A, alpha = beta = 90
degree, gamma = 120 degree. The asymmetric unit consists of two duplexes, each
one being complexed with two idarubicin drugs intercalated at the CpG steps, one
spermine and 160 water molecules. The molecular packing underlines major
groove-major groove interactions between neighbouring helices, and an unusually
low value of the occupied fraction of the unit cell due to a large solvent
channel of approximately 30 A diameter. This is the first trigonal crystal form
of a DNA-anthracycline complex. The structure is compared with the previously
reported structure of the same complex crystallizing in a tetragonal form. The
geometry of both the double helices and the intercalation site are conserved as
are the intramolecular interactions despite the different crystal forms.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.G.Byler,
C.Wang,
and
W.N.Setzer
(2009).
Quinoline alkaloids as intercalative topoisomerase inhibitors.
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J Mol Model,
15,
1417-1426.
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M.J.Araúzo-Bravo,
and
A.Sarai
(2008).
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation.
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Nucleic Acids Res,
36,
376-386.
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L.J.Ming
(2003).
Structure and function of "metalloantibiotics".
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Med Res Rev,
23,
697-762.
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C.Qian,
L.Lagacé,
M.J.Massariol,
C.Chabot,
C.Yoakim,
R.Déziel,
and
L.Tong
(2000).
A rational approach towards successful crystallization and crystal treatment of human cytomegalovirus protease and its inhibitor complex.
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Acta Crystallogr D Biol Crystallogr,
56,
175-180.
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P.Saminadin,
A.Dautant,
M.Mondon,
B.Langlois D'estaintot,
C.Courseille,
and
G.Précigoux
(2000).
Release of the cyano moiety in the crystal structure of N-cyanomethyl-N-(2-methoxyethyl)-daunomycin complexed with d(CGATCG).
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Eur J Biochem,
267,
457-464.
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PDB code:
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A.Adams,
J.M.Guss,
C.A.Collyer,
W.A.Denny,
and
L.P.Wakelin
(1999).
Crystal structure of the topoisomerase II poison 9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide bound to the DNA hexanucleotide d(CGTACG)2.
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Biochemistry,
38,
9221-9233.
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PDB code:
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S.Neidle,
and
C.M.Nunn
(1998).
Crystal structures of nucleic acids and their drug complexes.
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Nat Prod Rep,
15,
1.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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