DSSR-enabled G4 identification/annotation: PDB entry 7cps
Summary information and primary citation
- PDB-id
- 7cps
- Class
- DNA
- Method
- NMR
- Summary
- A 2:1 stoichiometric complex of anticancer drug 4'-epiadriamycin bound to parallel g-quadruplex DNA [d-(ttggggt)]4.
- Reference
- Barthwal R, Tariq Z, Pandav K: "A 2:1 stoichiometric complex of anticancer drug 4'-Epiadriamycin bound to parallel G-quadruplex DNA [d-(TTGGGGT)]4."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=3.-. groove=---- planarity=0.490 type=other -- nts=4 GGGG A.DG3,D.DG24,C.DG17,B.DG10 2 glyco-bond=---- sugar=---. groove=---- planarity=0.400 type=other -- nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11 3 glyco-bond=---- sugar=---- groove=---- planarity=0.562 type=bowl -- nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 4 glyco-bond=---- sugar=---- groove=---- planarity=0.674 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, 4 G-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=---- sugar=3.-. groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG24,C.DG17,B.DG10 2 glyco-bond=---- sugar=---. groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13 step#1 pm(>>,forward) area=17.16 rise=3.71 twist=18.4 step#2 pm(>>,forward) area=14.44 rise=3.75 twist=18.9 step#3 pm(>>,forward) area=8.74 rise=3.74 twist=27.4 strand#1 DNA glyco-bond=---- sugar=3--- nts=4 GGGG A.DG3,A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=---- sugar=.--- nts=4 GGGG D.DG24,D.DG25,D.DG26,D.DG27 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG17,C.DG18,C.DG19,C.DG20 strand#4 DNA glyco-bond=---- sugar=..-- nts=4 GGGG B.DG10,B.DG11,B.DG12,B.DG13 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=3.-. groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG24,C.DG17,B.DG10 |
|
2 glyco-bond=---- sugar=---. groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 |
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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=---- sugar=3.-. groove=---- WC-->Major -- nts=4 GGGG A.DG3,D.DG24,C.DG17,B.DG10 2 glyco-bond=---- sugar=---. groove=---- WC-->Major -- nts=4 GGGG A.DG4,D.DG25,C.DG18,B.DG11 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG5,D.DG26,C.DG19,B.DG12 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.DG6,D.DG27,C.DG20,B.DG13 step#1 pm(>>,forward) area=17.16 rise=3.71 twist=18.4 step#2 pm(>>,forward) area=14.44 rise=3.75 twist=18.9 step#3 pm(>>,forward) area=8.74 rise=3.74 twist=27.4 strand#1 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG A.DG3,A.DG4,A.DG5,A.DG6 strand#2 U DNA glyco-bond=---- sugar=.--- nts=4 GGGG D.DG24,D.DG25,D.DG26,D.DG27 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG17,C.DG18,C.DG19,C.DG20 strand#4 U DNA glyco-bond=---- sugar=..-- nts=4 GGGG B.DG10,B.DG11,B.DG12,B.DG13 |