DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 3eui
Class: DNA
Method: X-ray (2.2 Å)
Summary: A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine bsu-6042 in a large unit cell
Reference: Campbell NH, Patel M, Tofa AB, Ghosh R, Parkinson GN, Neidle S (2009): "Selectivity in Ligand Recognition of G-Quadruplex Loops." Biochemistry, 48, 1675-1680. doi: 10.1021/bi802233v.
Abstract: A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.
G4 notes: 4 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2

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

List of 4 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.246 type=bowl   -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.176 type=other  -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.174 type=other  -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23
 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.190 type=other  -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:A.DG9,1:B.DG24

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=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:A.DG9,1:B.DG24 step#1 mm(<>,outward) area=14.07 rise=3.50 twist=17.6 step#2 pp(><,inward) area=20.62 rise=3.59 twist=36.4 step#3 mm(<>,outward) area=12.65 rise=3.45 twist=19.6 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG16,1:B.DG15,1:B.DG14,1:B.DG13 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG21,1:B.DG22,1:B.DG23,1:B.DG24 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22 step#1 mm(<>,outward) area=14.07 rise=3.50 twist=17.6 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23 step#2 pp(><,inward) area=20.62 rise=3.59 twist=36.4 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:A.DG9,1:B.DG24 step#3 mm(<>,outward) area=12.65 rise=3.45 twist=19.6 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, 4 G-tetrads, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:A.DG9,1:B.DG24
  step#1  mm(<>,outward)  area=14.07 rise=3.50 twist=17.6
  step#2  pp(><,inward)   area=20.62 rise=3.59 twist=36.4
  step#3  mm(<>,outward)  area=12.65 rise=3.45 twist=19.6
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG16,1:B.DG15,1:B.DG14,1:B.DG13
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9
  strand#4  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG21,1:B.DG22,1:B.DG23,1:B.DG24
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT 1:A.DT5,1:A.DT6,1:A.DT7,1:A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT 1:B.DT17,1:B.DT18,1:B.DT19,1:B.DT20

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Interactive view in 3Dmol.js

DSSR-enabled G4 identification/annotation: PDB entry 3eui