DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 9c73
Class: DNA
Method: X-ray (1.66 Å)
Summary: Hybrid g-quadruplex from tetrahymena thermophila telomeric sequence in complex with trisqo
Reference: Ali A, Yatsunyk LA: "Hybrid G-quadruplex from Tetrahymena thermophila telomeric sequence in complex with triangular star shaped TrisQ ligand."
Abstract
G4 notes: 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)

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

List of 3 G-tetrads

 1 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.153 type=planar O+ nts=4 GGGG 1:A.DG5,1:A.DG10,1:A.DG18,1:A.DG23
 2 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.174 type=bowl-2 O+ nts=4 GGGG 1:A.DG6,1:A.DG11,1:A.DG17,1:A.DG24
 3 glyco-bond=--s- sugar=-3-- groove=-wn- planarity=0.272 type=bowl   O+ nts=4 GGGG 1:A.DG7,1:A.DG12,1:A.DG16,1:A.DG25

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, INTRA-molecular, with 1 stem

	1 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG5,1:A.DG10,1:A.DG18,1:A.DG23 2 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG6,1:A.DG11,1:A.DG17,1:A.DG24 3 glyco-bond=--s- sugar=-3-- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG7,1:A.DG12,1:A.DG16,1:A.DG25 step#1 pm(>>,forward) area=9.58 rise=3.44 twist=31.7 step#2 pm(>>,forward) area=13.81 rise=3.42 twist=25.7 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG5,1:A.DG6,1:A.DG7 strand#2 DNA glyco-bond=--- sugar=--3 nts=3 GGG 1:A.DG10,1:A.DG11,1:A.DG12 strand#3 DNA glyco-bond=sss sugar=--- nts=3 GGG 1:A.DG18,1:A.DG17,1:A.DG16 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG23,1:A.DG24,1:A.DG25 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG5,1:A.DG10,1:A.DG18,1:A.DG23 2 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG6,1:A.DG11,1:A.DG17,1:A.DG24 step#1 pm(>>,forward) area=9.58 rise=3.44 twist=31.7 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG6,1:A.DG11,1:A.DG17,1:A.DG24 3 glyco-bond=--s- sugar=-3-- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG7,1:A.DG12,1:A.DG16,1:A.DG25 step#2 pm(>>,forward) area=13.81 rise=3.42 twist=25.7 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-tetrads, 3 loops, INTRA-molecular, UUDU, hybrid1, 3+1, 3(-P-Lw-Ln)

 1  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG5,1:A.DG10,1:A.DG18,1:A.DG23
 2  glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG6,1:A.DG11,1:A.DG17,1:A.DG24
 3  glyco-bond=--s- sugar=-3-- groove=-wn- WC-->Major O+ nts=4 GGGG 1:A.DG7,1:A.DG12,1:A.DG16,1:A.DG25
  step#1  pm(>>,forward)  area=9.58  rise=3.44 twist=31.7
  step#2  pm(>>,forward)  area=13.81 rise=3.42 twist=25.7
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG5,1:A.DG6,1:A.DG7
  strand#2  U DNA glyco-bond=--- sugar=--3 nts=3 GGG 1:A.DG10,1:A.DG11,1:A.DG12
  strand#3  D DNA glyco-bond=sss sugar=--- nts=3 GGG 1:A.DG18,1:A.DG17,1:A.DG16
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG23,1:A.DG24,1:A.DG25
  loop#1 type=propeller strands=[#1,#2] nts=2 TT 1:A.DT8,1:A.DT9
  loop#2 type=lateral   strands=[#2,#3] nts=3 GTT 1:A.DG13,1:A.DT14,1:A.DT15
  loop#3 type=lateral   strands=[#3,#4] nts=4 GTTG 1:A.DG19,1:A.DT20,1:A.DT21,1:A.DG22

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Interactive view in 3Dmol.js

DSSR-enabled G4 identification/annotation: PDB entry 9c73