Summary information and primary citation

PDB-id
7csk
Class
DNA
Method
NMR
Summary
A 2:1 stoichiometric complex of anticancer drug adriamycin bound to parallel g-quadruplex DNA [d-(ttggggt)]4.
Reference
Barthwal R, Tariq Z, Pandav K: "A 2:1 stoichiometric complex of anticancer drug Adriamycin bound to parallel G-quadruplex DNA [d-(TTGGGGT)]4."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=3-33 groove=---- planarity=0.573 type=other  -- nts=4 GGGG A.DG3,D.DG25,C.DG18,B.DG10
 2 glyco-bond=---- sugar=3--- groove=---- planarity=0.782 type=bowl   -- nts=4 GGGG A.DG4,D.DG26,C.DG19,B.DG11
 3 glyco-bond=---- sugar=.--- groove=---- planarity=1.156 type=bowl   -- nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 3 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=---- sugar=3-33 groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG25,C.DG18,B.DG10
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG26,C.DG19,B.DG11
 3  glyco-bond=---- sugar=.--- groove=---- WC-->Major -- nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13
  step#1  pm(>>,forward)  area=16.72 rise=3.84 twist=8.9
  step#2  pm(>>,forward)  area=3.73  rise=6.07 twist=34.4
  strand#1 DNA glyco-bond=--- sugar=33. nts=3 GGG A.DG3,A.DG4,A.DG6
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG25,D.DG26,D.DG27
  strand#3 DNA glyco-bond=--- sugar=3-- nts=3 GGG C.DG18,C.DG19,C.DG20
  strand#4 DNA glyco-bond=--- sugar=3-- nts=3 GGG B.DG10,B.DG11,B.DG13

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2 stacking diagrams 
 1  glyco-bond=---- sugar=3-33 groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG25,C.DG18,B.DG10
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG26,C.DG19,B.DG11
  step#1  pm(>>,forward)  area=16.72 rise=3.84 twist=8.9

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 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG26,C.DG19,B.DG11
 3  glyco-bond=---- sugar=.--- groove=---- WC-->Major -- nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13
  step#2  pm(>>,forward)  area=3.73  rise=6.07 twist=34.4

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 3 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
 1  glyco-bond=---- sugar=3-33 groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG25,C.DG18,B.DG10
 2  glyco-bond=---- sugar=3--- groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG26,C.DG19,B.DG11
 3  glyco-bond=---- sugar=.--- groove=---- WC-->Major -- nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13
  step#1  pm(>>,forward)  area=16.72 rise=3.84 twist=8.9
  step#2  pm(>>,forward)  area=3.73  rise=6.07 twist=34.4
  strand#1* U DNA glyco-bond=--- sugar=33. nts=3 GGG A.DG3,A.DG4,A.DG6 bulged-nts=1 G A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG D.DG25,D.DG26,D.DG27
  strand#3  U DNA glyco-bond=--- sugar=3-- nts=3 GGG C.DG18,C.DG19,C.DG20
  strand#4* U DNA glyco-bond=--- sugar=3-- nts=3 GGG B.DG10,B.DG11,B.DG13 bulged-nts=1 G B.DG12

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