Detailed DSSR results for the G-quadruplex: PDB entry 3eui
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
- 3eui
- Class
- DNA
- Method
- X-ray (2.2 Å)
- Summary
- A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine bsu-6042 in a large unit cell
- Reference
- Campbell NH, Patel M, Tofa AB, Ghosh R, Parkinson GN, Neidle S (2009): "Selectivity in Ligand Recognition of G-Quadruplex Loops." Biochemistry, 48, 1675-1680. doi: 10.1021/bi802233v.
- Abstract
- A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.
- G4 notes
- 8 G-tetrads, 2 G4 helices, 2 G4 stems, (2+2), UDDU
Base-block schematics in six views
List of 8 G-tetrads
1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.246 type=bowl nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.176 type=other nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.174 type=other nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.190 type=other nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 5 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.277 type=bowl nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 6 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.209 type=other nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 7 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.179 type=other nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 8 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.211 type=other nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
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-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 step#1 mm(<>,outward) area=14.07 rise=3.50 twist=17.6 step#2 pp(><,inward) area=20.62 rise=3.59 twist=36.4 step#3 mm(<>,outward) area=12.65 rise=3.45 twist=19.6 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 |
 |
2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 |
 |
3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 |
Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48 step#1 mm(<>,outward) area=13.12 rise=3.50 twist=18.7 step#2 pp(><,inward) area=19.86 rise=3.54 twist=35.8 step#3 mm(<>,outward) area=12.56 rise=3.47 twist=19.5 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 |
 |
2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 |
 |
3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 |
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-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 step#1 mm(<>,outward) area=14.07 rise=3.50 twist=17.6 step#2 pp(><,inward) area=20.62 rise=3.59 twist=36.4 step#3 mm(<>,outward) area=12.65 rise=3.45 twist=19.6 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT B.DT17,B.DT18,B.DT19,B.DT20 |
Stem#2, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48 step#1 mm(<>,outward) area=13.12 rise=3.50 twist=18.7 step#2 pp(><,inward) area=19.86 rise=3.54 twist=35.8 step#3 mm(<>,outward) area=12.56 rise=3.47 twist=19.5 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT C.DT29,C.DT30,C.DT31,C.DT32 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT D.DT41,D.DT42,D.DT43,D.DT44 |