DSSR-enabled G4 identification/annotation: PDB entry 9e8e
Summary information and primary citation
- PDB-id
- 9e8e
- Class
- DNA
- Method
- X-ray (1.65 Å)
- Summary
- Hybrid g-quadruplex from tetrahymena thermophila telomeric sequence in complex with trisqo form 2
- 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=0.146 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=0.144 type=planar O+ nts=4 GGGG 1:A.DG6,1:A.DG11,1:A.DG17,1:A.DG24 3 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.286 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=---- 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=9.33 rise=3.37 twist=32.5 step#2 pm(>>,forward) area=14.78 rise=3.47 twist=25.5 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG5,1:A.DG6,1:A.DG7 strand#2 DNA glyco-bond=--- sugar=--- 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 |
| 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 |
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=---- 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=9.33 rise=3.37 twist=32.5 step#2 pm(>>,forward) area=14.78 rise=3.47 twist=25.5 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=--- 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 |