DSSR-enabled G4 identification/annotation: PDB entry 7xfv
Summary information and primary citation
- PDB-id
- 7xfv
- Class
- DNA
- Method
- NMR
- Summary
- Dimeric g-quadruplex DNA formed in the proximal promoter of vegfr-2
- Reference
- Zhang Y, Lan W, Wang C, Xue H, Cao C (2023): "Dimeric G-quadruplex DNA Structure in the Proximal Promoter of VEGFR-2 Reveals a New Drug Target to Inhibit Tumor Angiogenesis." Chin.J.Chem., 40, 2179-2187. doi: 10.1002/cjoc.202200260.
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.136 type=planar -- nts=4 GGGG A.DG3,A.DG5,B.DG17,B.DG19 2 glyco-bond=---- sugar=3.3. groove=---- planarity=0.054 type=planar -- nts=4 GGGG A.DG6,A.DG10,B.DG20,B.DG24 3 glyco-bond=---- sugar=3.3. groove=---- planarity=0.075 type=planar -- nts=4 GGGG A.DG7,A.DG11,B.DG21,B.DG25 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.097 type=planar -- nts=4 GGGG A.DG8,A.DG12,B.DG22,B.DG26
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-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG A.DG3,A.DG5,B.DG17,B.DG19 2 glyco-bond=---- sugar=.3.3 groove=---- WC-->Major -- nts=4 GGGG B.DG24,A.DG6,A.DG10,B.DG20 3 glyco-bond=---- sugar=.3.3 groove=---- WC-->Major -- nts=4 GGGG B.DG25,A.DG7,A.DG11,B.DG21 4 glyco-bond=---- sugar=3-3- groove=---- WC-->Major -- nts=4 GGGG B.DG26,A.DG8,A.DG12,B.DG22 step#1 pm(>>,forward) area=16.97 rise=4.45 twist=18.6 step#2 pm(>>,forward) area=12.93 rise=3.75 twist=28.8 step#3 pm(>>,forward) area=18.34 rise=3.95 twist=26.3 strand#1 DNA glyco-bond=---- sugar=-..3 nts=4 GGGG A.DG3,B.DG24,B.DG25,B.DG26 strand#2 DNA glyco-bond=---- sugar=333- nts=4 GGGG A.DG5,A.DG6,A.DG7,A.DG8 strand#3 DNA glyco-bond=---- sugar=-..3 nts=4 GGGG B.DG17,A.DG10,A.DG11,A.DG12 strand#4 DNA glyco-bond=---- sugar=333- nts=4 GGGG B.DG19,B.DG20,B.DG21,B.DG22 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG A.DG3,A.DG5,B.DG17,B.DG19 |
|
2 glyco-bond=---- sugar=.3.3 groove=---- WC-->Major -- nts=4 GGGG B.DG24,A.DG6,A.DG10,B.DG20 |
|
3 glyco-bond=---- sugar=.3.3 groove=---- WC-->Major -- nts=4 GGGG B.DG25,A.DG7,A.DG11,B.DG21 |
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-tetrads, 2 loops, inter-molecular, UUUU, parallel, 4+0
|
1 glyco-bond=---- sugar=3.3. groove=---- WC-->Major -- nts=4 GGGG A.DG6,A.DG10,B.DG20,B.DG24 2 glyco-bond=---- sugar=3.3. groove=---- WC-->Major -- nts=4 GGGG A.DG7,A.DG11,B.DG21,B.DG25 3 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG A.DG8,A.DG12,B.DG22,B.DG26 step#1 pm(>>,forward) area=12.93 rise=3.75 twist=28.8 step#2 pm(>>,forward) area=18.34 rise=3.95 twist=26.3 strand#1 U DNA glyco-bond=--- sugar=33- nts=3 GGG A.DG6,A.DG7,A.DG8 strand#2 U DNA glyco-bond=--- sugar=..3 nts=3 GGG A.DG10,A.DG11,A.DG12 strand#3 U DNA glyco-bond=--- sugar=33- nts=3 GGG B.DG20,B.DG21,B.DG22 strand#4 U DNA glyco-bond=--- sugar=..3 nts=3 GGG B.DG24,B.DG25,B.DG26 loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC9 loop#2 type=propeller strands=[#3,#4] nts=1 C B.DC23 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=3 GAG A.DG3,A.DA4,A.DG5 2 type=lateral helix=#1 nts=3 GAG B.DG17,B.DA18,B.DG19