Summary information and primary citation

PDB-id
9plb
Class
DNA
Method
X-ray (0.88 Å)
Summary
Jlm3 left-handed, parallel g-quadruplex in p1 21 1 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
4 G-tetrads, 1 G4 helix

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

PyMOL session file

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List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.183 type=other  O+ nts=4 GGGG A.DG1,A.DG4,A.DG8,A.DG11
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.230 type=other  O+ nts=4 GGGG A.DG3,A.DG6,A.DG10,A.DG13
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.185 type=other  O+ nts=4 GGGG B.DG1,B.DG4,B.DG8,B.DG11
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.225 type=other  O+ nts=4 GGGG B.DG3,B.DG6,B.DG10,B.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, 4 G-tetrads, inter-molecular
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG6,A.DG10,A.DG13
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG1
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG1,B.DG11,B.DG8,B.DG4
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG13,B.DG10,B.DG6,B.DG3
  step#1  mp(<<,backward) area=12.44 rise=3.31 twist=-25.9
  step#2  mm(<>,outward)  area=29.47 rise=3.29 twist=-11.3
  step#3  pm(>>,forward)  area=14.04 rise=3.38 twist=-24.3
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,B.DG1,B.DG13
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG6,A.DG8,B.DG11,B.DG10
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG10,A.DG11,B.DG8,B.DG6
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG13,A.DG1,B.DG4,B.DG3

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Interactive view in 3Dmol.js
3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG6,A.DG10,A.DG13
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG1
  step#1  mp(<<,backward) area=12.44 rise=3.31 twist=-25.9

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Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG11,A.DG1
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG1,B.DG11,B.DG8,B.DG4
  step#2  mm(<>,outward)  area=29.47 rise=3.29 twist=-11.3

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Interactive view in 3Dmol.js

 
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG1,B.DG11,B.DG8,B.DG4
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG13,B.DG10,B.DG6,B.DG3
  step#3  pm(>>,forward)  area=14.04 rise=3.38 twist=-24.3

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Interactive view in 3Dmol.js

List of 4 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
 3 type=V-shaped  helix=#1 nts=4 GTGG B.DG1,B.DT2,B.DG3,B.DG4
 4* type=V-shaped  helix=#1 nts=4 GGTG B.DG10,B.DG11,B.DT12,B.DG13