Detailed DSSR results for the G-quadruplex: PDB entry 6xrq
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
- 6xrq
- Class
- RNA
- Method
- X-ray (1.21 Å)
- Summary
- Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of pseudorabies virus
- Reference
- Zhang YS, Parkinson GN, Wei DG: "Structural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, parallel(4+0), UUUU, coaxial interfaces: 3'/5'
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=ssss sugar=3333 groove=---- planarity=0.179 type=other nts=4 GGGG B.G1,A.G6,A.G1,B.G6 2 glyco-bond=---- sugar=---- groove=---- planarity=0.143 type=planar nts=4 GGGG B.G2,B.G7,A.G2,A.G7 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.092 type=planar nts=4 GGGG B.G9,B.G12,A.G9,A.G12 4 glyco-bond=---- sugar=---3 groove=---- planarity=0.226 type=bowl-2 nts=4 GGGG B.G10,B.G13,A.G10,A.G13
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=ssss sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G1,A.G6,A.G1,B.G6 2* glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.G2,A.G7,A.G2,B.G7 3 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG B.G12,A.G9,A.G12,B.G9 4 glyco-bond=---- sugar=--3- groove=---- WC-->Major nts=4 GGGG B.G13,A.G10,A.G13,B.G10 step#1 mp(<<,backward) area=5.15 rise=3.29 twist=-45.4 step#2 mm(<>,outward) area=28.06 rise=3.36 twist=-8.6 step#3 pm(>>,forward) area=9.70 rise=3.38 twist=30.6 strand#1 RNA glyco-bond=s--- sugar=3-3- nts=4 GGGG B.G1,B.G2,B.G12,B.G13 strand#2 RNA glyco-bond=s--- sugar=3--- nts=4 GGGG A.G6,A.G7,A.G9,A.G10 strand#3 RNA glyco-bond=s--- sugar=3-33 nts=4 GGGG A.G1,A.G2,A.G12,A.G13 strand#4 RNA glyco-bond=s--- sugar=3--- nts=4 GGGG B.G6,B.G7,B.G9,B.G10 |
| 3 stacking diagrams | |
 |
1 glyco-bond=ssss sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G1,A.G6,A.G1,B.G6 |
 |
2* glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.G2,A.G7,A.G2,B.G7 |
 |
3 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG B.G12,A.G9,A.G12,B.G9 |
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, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=ssss sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G1,A.G6,A.G1,B.G6 2 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.G2,A.G7,A.G2,B.G7 step#1 mp(<<,backward) area=5.15 rise=3.29 twist=-45.4 strand#1 U RNA glyco-bond=s- sugar=3- nts=2 GG B.G1,B.G2 strand#2 U RNA glyco-bond=s- sugar=3- nts=2 GG A.G6,A.G7 strand#3 U RNA glyco-bond=s- sugar=3- nts=2 GG A.G1,A.G2 strand#4 U RNA glyco-bond=s- sugar=3- nts=2 GG B.G6,B.G7 loop#1 type=propeller strands=[#1,#4] nts=3 CUC B.C3,B.U4,B.C5 loop#2 type=propeller strands=[#3,#2] nts=3 CUC A.C3,A.U4,A.C5 |
Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG B.G9,B.G12,A.G9,A.G12 2 glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG B.G10,B.G13,A.G10,A.G13 step#1 pm(>>,forward) area=9.70 rise=3.38 twist=30.6 strand#1 U RNA glyco-bond=-- sugar=-- nts=2 GG B.G9,B.G10 strand#2 U RNA glyco-bond=-- sugar=3- nts=2 GG B.G12,B.G13 strand#3 U RNA glyco-bond=-- sugar=-- nts=2 GG A.G9,A.G10 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG A.G12,A.G13 loop#1 type=propeller strands=[#1,#2] nts=1 C B.C11 loop#2 type=propeller strands=[#3,#4] nts=1 C A.C11 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [3'/5']