Detailed DSSR results for the G-quadruplex: PDB entry 3ce5
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
- 3ce5
- Class
- DNA
- Method
- X-ray (2.5 Å)
- Summary
- A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule braco19
- Reference
- Campbell NH, Parkinson GN, Reszka AP, Neidle S (2008): "Structural basis of DNA quadruplex recognition by an acridine drug." J.Am.Chem.Soc., 130, 6722-6724. doi: 10.1021/ja8016973.
- Abstract
- The crystal structure of a complex between the bimolecular human telomeric quadruplex d(TAGGGTTAGGGT)2 and the experimental anticancer drug BRACO-19, has been determined, to 2.5 A resolution. The binding site for the BRACO-19 molecule is at the interface of two parallel-folded quadruplexes, sandwiched between a G-tetrad surface and a TATA tetrad, and held in the site by networks of water molecules. The structure rationalizes the existing structure-activity data and provides a starting-point for the structure-based design of quadruplex-binding ligands
- 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=--3- groove=---- planarity=0.154 type=planar nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- sugar=---- groove=---- planarity=0.203 type=other nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=-3-- groove=---- planarity=0.253 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=--3- 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=-3-- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=11.20 rise=3.37 twist=27.8 step#2 pm(>>,forward) area=12.37 rise=3.41 twist=27.8 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=--3 nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 DNA glyco-bond=--- sugar=3-- 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=--3- 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=--3- 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=-3-- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=11.20 rise=3.37 twist=27.8 step#2 pm(>>,forward) area=12.37 rise=3.41 twist=27.8 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=--3 nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 U DNA glyco-bond=--- sugar=3-- 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 |