Detailed DSSR results for the G-quadruplex: PDB entry 6jje
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
- 6jje
- Class
- DNA
- Method
- X-ray (1.378 Å)
- Summary
- Crystal structure of a two-quartet DNA mixed-parallel-antiparallel g-quadruplex (bru)
- Reference
- Zhang YS, Parkinson GN, Wagner A, Wei DG: "Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex (BrU)."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, (2+2), UDUD; parallel(4+0), UUUU, coaxial interfaces: mixed
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.180 type=other nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.266 type=bowl-2 nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 3 glyco-bond=---- sugar=---- groove=---- planarity=0.156 type=planar nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12 4 glyco-bond=---- sugar=---- groove=---- planarity=0.238 type=other nts=4 GGGG A.DG10,A.DG13,B.DG10,B.DG13
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, 4 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 2* glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG10,B.DG13,B.DG10,A.DG13 step#1 mm(<>,outward) area=19.25 rise=3.50 twist=12.2 step#2 pm(>>,forward) area=6.92 rise=3.21 twist=-38.3 step#3 pm(>>,forward) area=7.72 rise=3.26 twist=36.1 strand#1 DNA glyco-bond=-s-- sugar=---- nts=4 GGGG A.DG2,A.DG1,A.DG9,A.DG10 strand#2 DNA glyco-bond=s--- sugar=---- nts=4 GGGG A.DG6,A.DG7,B.DG12,B.DG13 strand#3 DNA glyco-bond=-s-- sugar=---- nts=4 GGGG B.DG2,B.DG1,B.DG9,B.DG10 strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG B.DG6,B.DG7,A.DG12,A.DG13 |
| 3 stacking diagrams | |
 |
1 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 |
 |
2* glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 |
 |
3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12 |
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, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)
 |
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7 2 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6 step#1 mm(<>,outward) area=19.25 rise=3.50 twist=12.2 strand#1 U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2 strand#2 D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG7,A.DG6 strand#3 U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2 strand#4 D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG7,B.DG6 loop#1 type=lateral strands=[#1,#2] nts=3 CuC A.DC3,A.BRU4,A.DC5 loop#2 type=lateral strands=[#3,#4] nts=3 CuC B.DC3,B.BRU4,B.DC5 |
Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG10,A.DG13,B.DG10,B.DG13 step#1 pm(>>,forward) area=7.72 rise=3.26 twist=36.1 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG9,A.DG10 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG12,A.DG13 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG9,B.DG10 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG12,B.DG13 loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC11 loop#2 type=propeller strands=[#3,#4] nts=1 C B.DC11 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [mixed]