Summary information and primary citation

PDB-id
9jo1
Class
DNA
Method
NMR
Summary
NMR solution structure of the 2:1 berberine-blm-g4 complex
Reference
Wang YY, Bian YT, Chen XY, Li JZ, Liu YS, Kong LY, Wang KB: "BLM G-quadruplex stabilizers synergize with PARP inhibitor to kill BRCA wild-type colon cancer cells."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)

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

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---. groove=---- planarity=0.144 type=planar O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG16
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.202 type=other  O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG17
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.198 type=other  O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG18

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=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG16
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG17
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG18
  step#1  pm(>>,forward)  area=12.02 rise=3.35 twist=29.7
  step#2  pm(>>,forward)  area=14.19 rise=3.39 twist=26.4
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG12,X.DG13,X.DG14
  strand#4 DNA glyco-bond=--- sugar=.-- nts=3 GGG X.DG16,X.DG17,X.DG18

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG16
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG17
  step#1  pm(>>,forward)  area=12.02 rise=3.35 twist=29.7

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG17
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG18
  step#2  pm(>>,forward)  area=14.19 rise=3.39 twist=26.4

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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, UUUU, parallel, 4+0, 3(-P-P-P)
 1  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG16
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG17
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG18
  step#1  pm(>>,forward)  area=12.02 rise=3.35 twist=29.7
  step#2  pm(>>,forward)  area=14.19 rise=3.39 twist=26.4
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG12,X.DG13,X.DG14
  strand#4  U DNA glyco-bond=--- sugar=.-- nts=3 GGG X.DG16,X.DG17,X.DG18
  loop#1 type=propeller strands=[#1,#2] nts=1 A X.DA7
  loop#2 type=propeller strands=[#2,#3] nts=1 C X.DC11
  loop#3 type=propeller strands=[#3,#4] nts=1 A X.DA15

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