Detailed DSSR results for the G-quadruplex: PDB entry 5mvb
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
- 5mvb
- Class
- DNA
- Method
- NMR
- Summary
- Solution structure of a human g-quadruplex hybrid-2 form in complex with a gold-ligand.
- Reference
- Wirmer-Bartoschek J, Bendel LE, Jonker HRA, Grun JT, Papi F, Bazzicalupi C, Messori L, Gratteri P, Schwalbe H (2017): "Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding." Angew. Chem. Int. Ed. Engl., 56, 7102-7106. doi: 10.1002/anie.201702135.
- Abstract
- Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand-G-quadruplex structure determination.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-Lw-Ln-P), hybrid-2(3+1), UDUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=s-ss sugar=..-- groove=wn-- planarity=0.348 type=bowl nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22 2 glyco-bond=-s-- sugar=---. groove=wn-- planarity=0.211 type=other nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 3 glyco-bond=-s-- sugar=---3 groove=wn-- planarity=0.307 type=bowl nts=4 GGGG A.DG6,A.DG10,A.DG18,A.DG24
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, INTRA-molecular, with 1 stem
 |
1 glyco-bond=s-ss sugar=..-- groove=wn-- Major-->WC nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22 2 glyco-bond=-s-- sugar=---. groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 3 glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG18,A.DG24 step#1 mm(<>,outward) area=14.78 rise=3.80 twist=11.8 step#2 pm(>>,forward) area=11.80 rise=3.91 twist=25.0 strand#1 DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=-ss sugar=.-- nts=3 GGG A.DG12,A.DG11,A.DG10 strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18 strand#4 DNA glyco-bond=s-- sugar=-.3 nts=3 GGG A.DG22,A.DG23,A.DG24 |
| 2 stacking diagrams | |
 |
1 glyco-bond=s-ss sugar=..-- groove=wn-- Major-->WC nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22 |
 |
2 glyco-bond=-s-- sugar=---. groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 |
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, 3 loops, INTRA-molecular, UDUU, hybrid-(mixed), 3(-Lw-Ln-P), hybrid-2(3+1)
 |
1 glyco-bond=s-ss sugar=..-- groove=wn-- Major-->WC nts=4 GGGG A.DG4,A.DG12,A.DG16,A.DG22 2 glyco-bond=-s-- sugar=---. groove=wn-- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 3 glyco-bond=-s-- sugar=---3 groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG10,A.DG18,A.DG24 step#1 mm(<>,outward) area=14.78 rise=3.80 twist=11.8 step#2 pm(>>,forward) area=11.80 rise=3.91 twist=25.0 strand#1 U DNA glyco-bond=s-- sugar=.-- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 D DNA glyco-bond=-ss sugar=.-- nts=3 GGG A.DG12,A.DG11,A.DG10 strand#3 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18 strand#4 U DNA glyco-bond=s-- sugar=-.3 nts=3 GGG A.DG22,A.DG23,A.DG24 loop#1 type=lateral strands=[#1,#2] nts=3 TTA A.DT7,A.DT8,A.DA9 loop#2 type=lateral strands=[#2,#3] nts=3 TTA A.DT13,A.DT14,A.DA15 loop#3 type=propeller strands=[#3,#4] nts=3 TTA A.DT19,A.DT20,A.DA21 |