Summary information and primary citation

PDB-id
9plc
Class
DNA
Method
X-ray (1.54 Å)
Summary
Jlm3 left-handed, parallel g-quadruplex in p65 2 2 spacegroup
Reference
Hendrickson AD, Xing E, Chen Y, Wang J, Yatsunyk LA, Mergny JL: "SubG4s: A Novel Class of Bulge-Rich G-Quadruplexes."
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix

Cartoon-block schematics in six views (download the tarball)

PyMOL session file

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List of 2 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=other  O+ nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.198 type=other  O+ nts=4 GGGG A.DG3,A.DG6,A.DG10,A.DG13

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, 2 G-tetrads, INTRA-molecular
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG3,A.DG6,A.DG10
  step#1  pm(>>,forward)  area=12.73 rise=3.31 twist=-25.8
  strand#1 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG1,A.DG13
  strand#2 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG4,A.DG3
  strand#3 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG6
  strand#4 DNA glyco-bond=-- sugar=-- nts=2 GG A.DG11,A.DG10

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Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG3,A.DG6,A.DG10
  step#1  pm(>>,forward)  area=12.73 rise=3.31 twist=-25.8

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Interactive view in 3Dmol.js

List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=V-shaped  helix=#1 nts=4 GTGG A.DG1,A.DT2,A.DG3,A.DG4
 2* type=V-shaped  helix=#1 nts=4 GGTG A.DG10,A.DG11,A.DT12,A.DG13