Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6jj0
Class
DNA
Method
NMR
Summary
NMR structure of the 1:1 complex of a carbazole derivative bmvc bound to c-myc G-quadruplex
Reference
Liu, W., Lin, C., Wu, G., Chang, T.C., Yang, D.: (2019) "Solution structures of the c-MYC Promoter G-quadruplex bound to a carbazole derivative: Insights into small molecule conformational switch for optimal G4-binding." Nucleic Acids Res.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

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List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.218 type=other  nts=4 GGGG A.DG7,A.DG11,A.DG16,A.DG20
 2 glyco-bond=---- groove=---- planarity=0.173 type=other  nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG21
 3 glyco-bond=---- groove=---- planarity=0.056 type=planar nts=4 GGGG A.DG9,A.DG13,A.DG18,A.DG22

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG7,A.DG11,A.DG16,A.DG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG21
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG13,A.DG18,A.DG22
  step#1  pm(>>,forward)  area=6.96  rise=3.62 twist=32.8
  step#2  pm(>>,forward)  area=12.94 rise=3.74 twist=26.5
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG20,A.DG21,A.DG22

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG7,A.DG11,A.DG16,A.DG20
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG21
step#1 pm(>>,forward) area=6.96 rise=3.62 twist=32.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG21
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG13,A.DG18,A.DG22
step#2 pm(>>,forward) area=12.94 rise=3.74 twist=26.5

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG7,A.DG11,A.DG16,A.DG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG8,A.DG12,A.DG17,A.DG21
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG13,A.DG18,A.DG22
  step#1  pm(>>,forward)  area=6.96  rise=3.62 twist=32.8
  step#2  pm(>>,forward)  area=12.94 rise=3.74 twist=26.5
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG20,A.DG21,A.DG22
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT10
  loop#2 type=propeller strands=[#2,#3] nts=2 TA A.DT14,A.DA15
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT19

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)