DSSR-enabled G4 identification/annotation: PDB entry 2gku
Summary information and primary citation
- PDB-id
- 2gku
- Class
- DNA
- Method
- NMR
- Summary
- Monomeric human telomere DNA tetraplex with 3+1 strand fold topology, two edgewise loops and double-chain reversal loop, NMR, 12 structures
- Reference
- Luu KN, Phan AT, Kuryavyi VV, Lacroix L, Patel DJ (2006): "Structure of the human telomere in k(+) solution: an intramolecular (3 + 1) g-quadruplex scaffold." J.Am.Chem.Soc., 128, 9963-9970. doi: 10.1021/ja062791w.
- Abstract
- We present the intramolecular G-quadruplex structure of human telomeric DNA in physiologically relevant K(+) solution. This G-quadruplex, whose (3 + 1) topology differs from folds reported previously in Na(+) solution and in a K(+)-containing crystal, involves the following: one anti.syn.syn.syn and two syn.anti.anti.anti G-tetrads; one double-chain reversal and two edgewise loops; three G-tracts oriented in one direction and the fourth in the opposite direction. The topological characteristics of this (3 + 1) G-quadruplex scaffold should provide a unique platform for structure-based anticancer drug design targeted to human telomeric DNA.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-Lw-Ln), hybrid-1(3+1), UUDU
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=ss-s sugar=---. groove=-wn- planarity=0.161 type=other O- nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21 2 glyco-bond=--s- sugar=---. groove=-wn- planarity=0.141 type=planar O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=--s- sugar=--3- groove=-wn- planarity=0.233 type=bowl O+ nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23
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-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=ss-s sugar=---. groove=-wn- Major-->WC O- nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21 2 glyco-bond=--s- sugar=---. groove=-wn- WC-->Major O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=--s- sugar=--3- groove=-wn- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23 step#1 mm(<>,outward) area=14.24 rise=3.58 twist=16.8 step#2 pm(>>,forward) area=13.12 rise=3.71 twist=25.9 strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 DNA glyco-bond=-ss sugar=--3 nts=3 GGG A.DG17,A.DG16,A.DG15 strand#4 DNA glyco-bond=s-- sugar=..- nts=3 GGG A.DG21,A.DG22,A.DG23 |
| 2 stacking diagrams | |
|
1 glyco-bond=ss-s sugar=---. groove=-wn- Major-->WC O- nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21 |
|
2 glyco-bond=--s- sugar=---. groove=-wn- WC-->Major O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 |
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, 3 loops, INTRA-molecular, UUDU, hybrid-(mixed), 3(-P-Lw-Ln), hybrid-1(3+1)
|
1 glyco-bond=ss-s sugar=---. groove=-wn- Major-->WC O- nts=4 GGGG A.DG3,A.DG9,A.DG17,A.DG21 2 glyco-bond=--s- sugar=---. groove=-wn- WC-->Major O+ nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 3 glyco-bond=--s- sugar=--3- groove=-wn- WC-->Major O+ nts=4 GGGG A.DG5,A.DG11,A.DG15,A.DG23 step#1 mm(<>,outward) area=14.24 rise=3.58 twist=16.8 step#2 pm(>>,forward) area=13.12 rise=3.71 twist=25.9 strand#1 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 D DNA glyco-bond=-ss sugar=--3 nts=3 GGG A.DG17,A.DG16,A.DG15 strand#4 U DNA glyco-bond=s-- sugar=..- nts=3 GGG A.DG21,A.DG22,A.DG23 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=lateral strands=[#2,#3] nts=3 TTA A.DT12,A.DT13,A.DA14 loop#3 type=lateral strands=[#3,#4] nts=3 TTA A.DT18,A.DT19,A.DA20 |