Detailed DSSR results for the G-quadruplex: PDB entry 4p1d
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 4p1d
- Class
- DNA
- Method
- X-ray (1.55 Å)
- Summary
- Structure of the complex of a bimolecular human telomeric DNA with coptisine
- Reference
- Ferraroni M, Bazzicalupi C, Gratteri P, Bilia AR, Sissi C: "Crystal Structure of the complex of a bimolecular human telomeric DNA with Coptisine."
- Abstract
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.138 type=planar nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- sugar=---- groove=---- planarity=0.136 type=planar nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- planarity=0.264 type=bowl nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
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-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=8.61 rise=3.32 twist=32.3 step#2 pm(>>,forward) area=12.50 rise=3.43 twist=26.5 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG21,B.DG22,B.DG23 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 |
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-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=8.61 rise=3.32 twist=32.3 step#2 pm(>>,forward) area=12.50 rise=3.43 twist=26.5 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG21,B.DG22,B.DG23 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=propeller strands=[#3,#4] nts=3 TTA B.DT18,B.DT19,B.DA20 |