DSSR-enabled G4 identification/annotation: PDB entry 8twh
Summary information and primary citation
- PDB-id
- 8twh
- Class
- DNA
- Method
- X-ray (2.47 Å)
- Summary
- Crystal structure of (gggtt)3ggg g-quadruplex in complex with small molecule ligand rhps4
- Reference
- Lam G, Martin KN, Yatsunyk LA: "Crystal structure of (GGGTT)3GGG G-quadruplex in complex with small molecule ligand RHPS4."
- Abstract
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.071 type=planar O+ nts=4 GGGG 1:A.DG1,1:A.DG6,1:A.DG11,1:A.DG16 2 glyco-bond=---- sugar=---- groove=---- planarity=0.080 type=planar O+ nts=4 GGGG 1:A.DG2,1:A.DG7,1:A.DG12,1:A.DG17 3 glyco-bond=---- sugar=---- groove=---- planarity=0.274 type=bowl O+ nts=4 GGGG 1:A.DG3,1:A.DG8,1:A.DG13,1:A.DG18
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
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG6,1:A.DG11,1:A.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG7,1:A.DG12,1:A.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG8,1:A.DG13,1:A.DG18 step#1 pm(>>,forward) area=8.36 rise=3.27 twist=34.1 step#2 pm(>>,forward) area=17.95 rise=3.48 twist=22.4 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG1,1:A.DG2,1:A.DG3 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG6,1:A.DG7,1:A.DG8 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG11,1:A.DG12,1:A.DG13 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG16,1:A.DG17,1:A.DG18 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG6,1:A.DG11,1:A.DG16 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG7,1:A.DG12,1:A.DG17 |
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, UUUU, parallel, 4+0, 3(-P-P-P)
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG6,1:A.DG11,1:A.DG16 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG7,1:A.DG12,1:A.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG8,1:A.DG13,1:A.DG18 step#1 pm(>>,forward) area=8.36 rise=3.27 twist=34.1 step#2 pm(>>,forward) area=17.95 rise=3.48 twist=22.4 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG1,1:A.DG2,1:A.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG6,1:A.DG7,1:A.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG11,1:A.DG12,1:A.DG13 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG16,1:A.DG17,1:A.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 TT 1:A.DT4,1:A.DT5 loop#2 type=propeller strands=[#2,#3] nts=2 TT 1:A.DT9,1:A.DT10 loop#3 type=propeller strands=[#3,#4] nts=2 TT 1:A.DT14,1:A.DT15 |