DSSR-enabled G4 identification/annotation: PDB entry 3tvb
Summary information and primary citation
- PDB-id
- 3tvb
- Class
- DNA-antibiotic
- Method
- X-ray (1.08 Å)
- Summary
- A highly symmetric DNA g-4 quadruplex-drug complex
- Reference
- Clark GR, Pytel PD, Squire CJ (2012): "The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages." Nucleic Acids Res., 40, 5731-5738. doi: 10.1093/nar/gks193.
- Abstract
- We have determined the X-ray structure of the complex between the DNA quadruplex d(5'-GGGG-3')(4) and daunomycin, as a potential model for studying drug-telomere interactions. The structure was solved at 1.08 Å by direct methods in space group I4. The asymmetric unit comprises a linear arrangement of one d(GGGG) strand, four daunomycin molecules, a second d(GGGG) strand facing in the opposite direction to the first, and Na and Mg cations. The crystallographic 4-fold axis generates the biological unit, which is a 12-layered structure comprising two sets of four guanine layers, with four layers each of four daunomycins stacked between the 5' faces of the two quadruplexes. The daunomycin layers fall into two groups which are novel in their mode of self assembly. The only contacts between daunomycin molecules within any one of these layers are van der Waals interactions, however there is substantial π-π stacking between successive daunomycin layers and also with adjacent guanine layers. The structure differs significantly from all other parallel d(TGGGGT)(4) quadruplexes in that the 5' guanine adopts the unusual syn glycosyl linkage, refuting the widespread belief that such conformations should all be anti. In contrast to the related d(TGGGGT)/daunomycin complex, there are no ligand-quadruplex groove insertion interactions.
- G4 notes
- 8 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
List of 8 G-tetrads
1 glyco-bond=ssss sugar=---- groove=---- planarity=0.075 type=planar -- nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1 2 glyco-bond=---- sugar=---- groove=---- planarity=0.198 type=other -- nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2 3 glyco-bond=---- sugar=---- groove=---- planarity=0.108 type=planar -- nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3 4 glyco-bond=---- sugar=---- groove=---- planarity=0.312 type=bowl -- nts=4 GGGG 1:A.DG4,4:A.DG4,2:A.DG4,3:A.DG4 5 glyco-bond=ssss sugar=---- groove=---- planarity=0.060 type=planar -- nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5 6 glyco-bond=---- sugar=---- groove=---- planarity=0.163 type=other -- nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6 7 glyco-bond=---- sugar=---- groove=---- planarity=0.098 type=planar -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 8 glyco-bond=---- sugar=---- groove=---- planarity=0.311 type=bowl -- nts=4 GGGG 1:B.DG8,3:B.DG8,2:B.DG8,4:B.DG8
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, 4 G-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,4:A.DG4,2:A.DG4,3:A.DG4 step#1 mm(<>,outward) area=12.41 rise=3.45 twist=20.5 step#2 pm(>>,forward) area=9.06 rise=3.21 twist=33.7 step#3 pm(>>,forward) area=14.52 rise=3.45 twist=22.2 strand#1 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4 strand#2 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 4:A.DG1,4:A.DG2,4:A.DG3,4:A.DG4 strand#3 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 2:A.DG1,2:A.DG2,2:A.DG3,2:A.DG4 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 3:A.DG1,3:A.DG2,3:A.DG3,3:A.DG4 |
| 3 stacking diagrams | |
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3 |
Helix#2, 4 G-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG8,3:B.DG8,2:B.DG8,4:B.DG8 step#1 mm(<>,outward) area=11.40 rise=3.46 twist=22.1 step#2 pm(>>,forward) area=9.24 rise=3.22 twist=33.3 step#3 pm(>>,forward) area=14.60 rise=3.47 twist=22.8 strand#1 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 1:B.DG5,1:B.DG6,1:B.DG7,1:B.DG8 strand#2 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 3:B.DG5,3:B.DG6,3:B.DG7,3:B.DG8 strand#3 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 2:B.DG5,2:B.DG6,2:B.DG7,2:B.DG8 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG 4:B.DG5,4:B.DG6,4:B.DG7,4:B.DG8 |
| 3 stacking diagrams | |
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 |
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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:A.DG1,4:A.DG1,2:A.DG1,3:A.DG1 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,4:A.DG2,2:A.DG2,3:A.DG2 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,4:A.DG3,2:A.DG3,3:A.DG3 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,4:A.DG4,2:A.DG4,3:A.DG4 step#1 mm(<>,outward) area=12.41 rise=3.45 twist=20.5 step#2 pm(>>,forward) area=9.06 rise=3.21 twist=33.7 step#3 pm(>>,forward) area=14.52 rise=3.45 twist=22.2 strand#1 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4 strand#2 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 4:A.DG1,4:A.DG2,4:A.DG3,4:A.DG4 strand#3 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 2:A.DG1,2:A.DG2,2:A.DG3,2:A.DG4 strand#4 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 3:A.DG1,3:A.DG2,3:A.DG3,3:A.DG4 |
Stem#2, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=ssss sugar=---- groove=---- Major-->WC -- nts=4 GGGG 1:B.DG5,3:B.DG5,2:B.DG5,4:B.DG5 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG6,3:B.DG6,2:B.DG6,4:B.DG6 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG7,3:B.DG7,2:B.DG7,4:B.DG7 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:B.DG8,3:B.DG8,2:B.DG8,4:B.DG8 step#1 mm(<>,outward) area=11.40 rise=3.46 twist=22.1 step#2 pm(>>,forward) area=9.24 rise=3.22 twist=33.3 step#3 pm(>>,forward) area=14.60 rise=3.47 twist=22.8 strand#1 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 1:B.DG5,1:B.DG6,1:B.DG7,1:B.DG8 strand#2 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 3:B.DG5,3:B.DG6,3:B.DG7,3:B.DG8 strand#3 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 2:B.DG5,2:B.DG6,2:B.DG7,2:B.DG8 strand#4 U DNA glyco-bond=s--- sugar=---- nts=4 GGGG 4:B.DG5,4:B.DG6,4:B.DG7,4:B.DG8 |