Summary information

PDB id
8kf9
Class
DNA
Method
NMR
Summary
Stable g-quadruplex conformation formed in promoter region of oncogene ret in 50 mm k+ solution
Reference
Zhang YP, Lan WX, Yin SW, Liu ZJ, Xue HJ, Cao CY: "Stable G-quadruplex Conformation Formed in Promoter Region of Oncogene RET Indicates New Target for Anti-cancer Drug Screening."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(D+PX), UD3(1+3), UDDD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s--- sugar=3.-. groove=w--n planarity=0.193 type=other  nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 2 glyco-bond=-ss- sugar=-.-. groove=w-n- planarity=0.196 type=other  nts=4 GGGG A.DG2,A.DG11,A.DG7,A.DG17
 3 glyco-bond=--s- sugar=--3. groove=-wn- planarity=0.221 type=other  nts=4 GGGG A.DG9,A.DG13,A.DG16,A.DG19

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=-ss- sugar=-.-. groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG7,A.DG17
 2  glyco-bond=s--- sugar=3.-. groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 3  glyco-bond=s--- sugar=3--. groove=w--n Major-->WC nts=4 GGGG A.DG16,A.DG13,A.DG9,A.DG19
  step#1  mm(<>,outward)  area=10.27 rise=3.49 twist=25.2
  step#2  pm(>>,forward)  area=15.46 rise=3.29 twist=28.7
  strand#1 DNA glyco-bond=-ss sugar=-33 nts=3 GGG A.DG2,A.DG1,A.DG16
  strand#2 DNA glyco-bond=s-- sugar=..- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#4 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams 
 1  glyco-bond=-ss- sugar=-.-. groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG7,A.DG17
 2  glyco-bond=s--- sugar=3.-. groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
  step#1  mm(<>,outward)  area=10.27 rise=3.49 twist=25.2

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 2  glyco-bond=s--- sugar=3.-. groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 3  glyco-bond=s--- sugar=3--. groove=w--n Major-->WC nts=4 GGGG A.DG16,A.DG13,A.DG9,A.DG19
  step#2  pm(>>,forward)  area=15.46 rise=3.29 twist=28.7

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 2(D+PX), UD3(1+3)

 1  glyco-bond=s--- sugar=3.-. groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG12,A.DG8,A.DG18
 2  glyco-bond=-ss- sugar=-.-. groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG11,A.DG7,A.DG17
  step#1  mm(<>,outward)  area=10.27 rise=3.49 twist=25.2
  strand#1  U DNA glyco-bond=s- sugar=3- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=.. nts=2 GG A.DG12,A.DG11
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG8,A.DG7
  strand#4  D DNA glyco-bond=-- sugar=.. nts=2 GG A.DG18,A.DG17
  loop#1 type=diagonal  strands=[#1,#3] nts=4 GTAG A.DG3,A.DT4,A.DA5,A.DG6
  loop#2 type=propeller strands=[#3,#2] nts=2 GC A.DG9,A.DC10
  loop#3 type=diag-prop strands=[#2,#4] nts=4 GGCG A.DG13,A.DG14,A.DC15,A.DG16

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

 1 type=lateral   helix=#1 nts=4 GGCG A.DG13,A.DG14,A.DC15,A.DG16
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG16,A.DG17,A.DG18,A.DG19