DSSR-enabled G4 identification/annotation: PDB entry 2gwq
Summary information and primary citation
- PDB-id
- 2gwq
- Class
- DNA
- Method
- X-ray (2.0 Å)
- Summary
- Crystal structure of d(g4t4g4) with four quadruplexes in the asymmetric unit.
- Reference
- Lee MPH, Haider S, Parkinson GN, Neidle S: "Crystal structure of D(G4T4G4) with four and six quadruplexes in the asymmetric unit."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.255 type=bowl -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.116 type=planar -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.112 type=planar -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.240 type=other -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:A.DG9,1:B.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, 4 G-tetrads, inter-molecular, with 1 stem
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1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:A.DG9,1:B.DG24 step#1 mm(<>,outward) area=14.33 rise=3.49 twist=17.3 step#2 pp(><,inward) area=20.17 rise=3.56 twist=36.5 step#3 mm(<>,outward) area=13.64 rise=3.46 twist=17.9 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG16,1:B.DG15,1:B.DG14,1:B.DG13 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG21,1:B.DG22,1:B.DG23,1:B.DG24 |
| 3 stacking diagrams | |
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1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21 |
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2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22 |
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3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.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, 4 G-tetrads, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2
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1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG1,1:B.DG16,1:A.DG12,1:B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG2,1:B.DG15,1:A.DG11,1:B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:A.DG3,1:B.DG14,1:A.DG10,1:B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:A.DG4,1:B.DG13,1:A.DG9,1:B.DG24 step#1 mm(<>,outward) area=14.33 rise=3.49 twist=17.3 step#2 pp(><,inward) area=20.17 rise=3.56 twist=36.5 step#3 mm(<>,outward) area=13.64 rise=3.46 twist=17.9 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG3,1:A.DG4 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:B.DG16,1:B.DG15,1:B.DG14,1:B.DG13 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:A.DG12,1:A.DG11,1:A.DG10,1:A.DG9 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:B.DG21,1:B.DG22,1:B.DG23,1:B.DG24 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT 1:A.DT5,1:A.DT6,1:A.DT7,1:A.DT8 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT 1:B.DT17,1:B.DT18,1:B.DT19,1:B.DT20 |