Summary information

PDB id
6kxz
Class
DNA
Method
NMR
Summary
Human parallel stranded 7-mer g-quadruplex complexed with 2 epirubicin (epi) molecules
Reference
Barthwal R, Raje S, Pandav K: "HUMAN PARALLEL STRANDED 7-MER G-QUADRUPLEX COMPLEXED WITH 2 EPIRUBICIN (DM6) MOLECULES."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---- groove=---- planarity=0.803 type=other  nts=4 GGGG A.DG4,B.DG11,C.DG18,D.DG25
 2 glyco-bond=---- groove=---- planarity=0.796 type=other  nts=4 GGGG A.DG5,B.DG12,C.DG19,D.DG26
 3 glyco-bond=---- groove=---- planarity=0.859 type=other  nts=4 GGGG A.DG6,B.DG13,C.DG20,D.DG27

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-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG4,B.DG11,C.DG18,D.DG25
 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG5,B.DG12,C.DG19,D.DG26
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG6,B.DG13,C.DG20,D.DG27
  step#1  pm(>>,forward)  area=12.71 rise=3.93 twist=21.9
  step#2  pm(>>,forward)  area=7.22  rise=4.19 twist=21.7
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#3 DNA glyco-bond=--- nts=3 GGG C.DG18,C.DG19,C.DG20
  strand#4 DNA glyco-bond=--- nts=3 GGG D.DG25,D.DG26,D.DG27

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG4,B.DG11,C.DG18,D.DG25
2 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG5,B.DG12,C.DG19,D.DG26
step#1 pm(>>,forward) area=12.71 rise=3.93 twist=21.9

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG5,B.DG12,C.DG19,D.DG26
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG6,B.DG13,C.DG20,D.DG27
step#2 pm(>>,forward) area=7.22 rise=4.19 twist=21.7

Download PDB file
Interactive view in 3Dmol.js

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-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG4,B.DG11,C.DG18,D.DG25
 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG5,B.DG12,C.DG19,D.DG26
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG6,B.DG13,C.DG20,D.DG27
  step#1  pm(>>,forward)  area=12.71 rise=3.93 twist=21.9
  step#2  pm(>>,forward)  area=7.22  rise=4.19 twist=21.7
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#3  U DNA glyco-bond=--- nts=3 GGG C.DG18,C.DG19,C.DG20
  strand#4  U DNA glyco-bond=--- nts=3 GGG D.DG25,D.DG26,D.DG27

Download PDB file
Interactive view in 3Dmol.js