DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 3ce5
Class: DNA
Method: X-ray (2.5 Å)
Summary: A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule braco19
Reference: Campbell NH, Parkinson GN, Reszka AP, Neidle S (2008): "Structural basis of DNA quadruplex recognition by an acridine drug." J.Am.Chem.Soc., 130, 6722-6724. doi: 10.1021/ja8016973.
Abstract: The crystal structure of a complex between the bimolecular human telomeric quadruplex d(TAGGGTTAGGGT)2 and the experimental anticancer drug BRACO-19, has been determined, to 2.5 A resolution. The binding site for the BRACO-19 molecule is at the interface of two parallel-folded quadruplexes, sandwiched between a G-tetrad surface and a TATA tetrad, and held in the site by networks of water molecules. The structure rationalizes the existing structure-activity data and provides a starting-point for the structure-based design of quadruplex-binding ligands
G4 notes: 6 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0

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

List of 6 G-tetrads

 1 glyco-bond=---- sugar=--3- groove=---- planarity=0.154 type=planar -- nts=4 GGGG 1:A.DG3,1:A.DG9,1:B.DG15,1:B.DG21
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.203 type=other  -- nts=4 GGGG 1:A.DG4,1:A.DG10,1:B.DG16,1:B.DG22
 3 glyco-bond=---- sugar=-3-- groove=---- planarity=0.253 type=bowl   -- nts=4 GGGG 1:A.DG5,1:A.DG11,1:B.DG17,1:B.DG23
 4 glyco-bond=---- sugar=--3- groove=---- planarity=0.154 type=planar -- nts=4 GGGG 2:A.DG3,2:A.DG9,2:B.DG15,2:B.DG21
 5 glyco-bond=---- sugar=---- groove=---- planarity=0.203 type=other  -- nts=4 GGGG 2:A.DG4,2:A.DG10,2:B.DG16,2:B.DG22
 6 glyco-bond=---- sugar=-3-- groove=---- planarity=0.253 type=bowl   -- nts=4 GGGG 2:A.DG5,2:A.DG11,2:B.DG17,2:B.DG23

List of 2 G4-helices

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- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:A.DG9,1:B.DG15,1:B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG10,1:B.DG16,1:B.DG22 3 glyco-bond=---- sugar=-3-- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:A.DG11,1:B.DG17,1:B.DG23 step#1 pm(>>,forward) area=11.20 rise=3.37 twist=27.8 step#2 pm(>>,forward) area=12.37 rise=3.41 twist=27.8 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG3,1:A.DG4,1:A.DG5 strand#2 DNA glyco-bond=--- sugar=--3 nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11 strand#3 DNA glyco-bond=--- sugar=3-- nts=3 GGG 1:B.DG15,1:B.DG16,1:B.DG17 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG21,1:B.DG22,1:B.DG23 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=--3- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:A.DG9,1:B.DG15,1:B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG10,1:B.DG16,1:B.DG22 step#1 pm(>>,forward) area=11.20 rise=3.37 twist=27.8 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG10,1:B.DG16,1:B.DG22 3 glyco-bond=---- sugar=-3-- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:A.DG11,1:B.DG17,1:B.DG23 step#2 pm(>>,forward) area=12.37 rise=3.41 twist=27.8 Download PDB file Interactive view in 3Dmol.js

Helix#2, 3 G-tetrads, inter-molecular, with 1 stem

	1 glyco-bond=---- sugar=--3- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG3,2:A.DG9,2:B.DG15,2:B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG4,2:A.DG10,2:B.DG16,2:B.DG22 3 glyco-bond=---- sugar=-3-- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG5,2:A.DG11,2:B.DG17,2:B.DG23 step#1 pm(>>,forward) area=11.20 rise=3.37 twist=27.8 step#2 pm(>>,forward) area=12.37 rise=3.41 twist=27.8 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG3,2:A.DG4,2:A.DG5 strand#2 DNA glyco-bond=--- sugar=--3 nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11 strand#3 DNA glyco-bond=--- sugar=3-- nts=3 GGG 2:B.DG15,2:B.DG16,2:B.DG17 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:B.DG21,2:B.DG22,2:B.DG23 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=--3- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG3,2:A.DG9,2:B.DG15,2:B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG4,2:A.DG10,2:B.DG16,2:B.DG22 step#1 pm(>>,forward) area=11.20 rise=3.37 twist=27.8 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG4,2:A.DG10,2:B.DG16,2:B.DG22 3 glyco-bond=---- sugar=-3-- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG5,2:A.DG11,2:B.DG17,2:B.DG23 step#2 pm(>>,forward) area=12.37 rise=3.41 twist=27.8 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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, 2 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=--3- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:A.DG9,1:B.DG15,1:B.DG21
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:A.DG10,1:B.DG16,1:B.DG22
 3  glyco-bond=---- sugar=-3-- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:A.DG11,1:B.DG17,1:B.DG23
  step#1  pm(>>,forward)  area=11.20 rise=3.37 twist=27.8
  step#2  pm(>>,forward)  area=12.37 rise=3.41 twist=27.8
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG3,1:A.DG4,1:A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--3 nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11
  strand#3  U DNA glyco-bond=--- sugar=3-- nts=3 GGG 1:B.DG15,1:B.DG16,1:B.DG17
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG21,1:B.DG22,1:B.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA 1:A.DT6,1:A.DT7,1:A.DA8
  loop#2 type=propeller strands=[#3,#4] nts=3 TTA 1:B.DT18,1:B.DT19,1:B.DA20

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 3 G-tetrads, 2 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=--3- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG3,2:A.DG9,2:B.DG15,2:B.DG21
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG4,2:A.DG10,2:B.DG16,2:B.DG22
 3  glyco-bond=---- sugar=-3-- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG5,2:A.DG11,2:B.DG17,2:B.DG23
  step#1  pm(>>,forward)  area=11.20 rise=3.37 twist=27.8
  step#2  pm(>>,forward)  area=12.37 rise=3.41 twist=27.8
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG3,2:A.DG4,2:A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--3 nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11
  strand#3  U DNA glyco-bond=--- sugar=3-- nts=3 GGG 2:B.DG15,2:B.DG16,2:B.DG17
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG 2:B.DG21,2:B.DG22,2:B.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA 2:A.DT6,2:A.DT7,2:A.DA8
  loop#2 type=propeller strands=[#3,#4] nts=3 TTA 2:B.DT18,2:B.DT19,2:B.DA20