Summary information and primary citation

PDB-id
26jr
Class
DNA
Method
NMR
Summary
NMR solution structures of mtr-106-myt1lcomplex
Reference
Li Y, Liu K, Hu X, Deng J, Lan W, Xue H, Tang W, Cao C (2026): "Structural insights into the binding of CX-5461 and MTR-106 to G-quadruplex DNA." Nucleic Acids Res., 54. doi: 10.1093/nar/gkag667.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)

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

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List of 3 G-tetrads

 1 glyco-bond=s-ss sugar=-.-3 groove=wn-- planarity=0.085 type=planar O- nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2 glyco-bond=-s-- sugar=3.-. groove=wn-- planarity=0.038 type=planar O+ nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3 glyco-bond=-s-- sugar=3..3 groove=wn-- planarity=0.041 type=planar O+ nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29

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=s-ss sugar=-.-3 groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2  glyco-bond=-s-- sugar=3.-. groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3  glyco-bond=-s-- sugar=3..3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29
  step#1  mm(<>,outward)  area=14.21 rise=3.90 twist=19.8
  step#2  pm(>>,forward)  area=15.72 rise=3.65 twist=25.2
  strand#1 DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-ss sugar=... nts=3 GGG A.DG20,A.DG19,A.DG18
  strand#3 DNA glyco-bond=s-- sugar=--. nts=3 GGG A.DG23,A.DG24,A.DG25
  strand#4 DNA glyco-bond=s-- sugar=3.3 nts=3 GGG A.DG27,A.DG28,A.DG29

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2 stacking diagrams 
 1  glyco-bond=s-ss sugar=-.-3 groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2  glyco-bond=-s-- sugar=3.-. groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
  step#1  mm(<>,outward)  area=14.21 rise=3.90 twist=19.8

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 2  glyco-bond=-s-- sugar=3.-. groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3  glyco-bond=-s-- sugar=3..3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29
  step#2  pm(>>,forward)  area=15.72 rise=3.65 twist=25.2

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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, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)
 1  glyco-bond=s-ss sugar=-.-3 groove=wn-- Major-->WC O- nts=4 GGGG A.DG2,A.DG20,A.DG23,A.DG27
 2  glyco-bond=-s-- sugar=3.-. groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG19,A.DG24,A.DG28
 3  glyco-bond=-s-- sugar=3..3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG18,A.DG25,A.DG29
  step#1  mm(<>,outward)  area=14.21 rise=3.90 twist=19.8
  step#2  pm(>>,forward)  area=15.72 rise=3.65 twist=25.2
  strand#1  U DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-ss sugar=... nts=3 GGG A.DG20,A.DG19,A.DG18
  strand#3  U DNA glyco-bond=s-- sugar=--. nts=3 GGG A.DG23,A.DG24,A.DG25
  strand#4  U DNA glyco-bond=s-- sugar=3.3 nts=3 GGG A.DG27,A.DG28,A.DG29
  loop#1 type=lateral   strands=[#1,#2] nts=13 AGAGGAGAGCTCT A.DA5,A.DG6,A.DA7,A.DG8,A.DG9,A.DA10,A.DG11,A.DA12,A.DG13,A.DC14,A.DT15,A.DC16,A.DT17
  loop#2 type=lateral   strands=[#2,#3] nts=2 TT A.DT21,A.DT22
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT26

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