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

PDB-id
6suu
Class
DNA
Method
NMR
Summary
NMR structure of kras32r g9t conformer G-quadruplex within kras promoter region
Reference
Marquevielle, J., Robert, C., Lagrabette, O., Wahid, M., Bourdoncle, A., Xodo, L., Mergny, J.L., Salgado, G.: "Structure of Multiple G-quadruplexes in equilibrium in KRAS promoter region." To be published
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-P-P-P), parallel(4+0), UUUU

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

PyMOL session file PDB file View in 3Dmol.js

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

 1 glyco-bond=---- groove=---- planarity=0.677 type=bowl   nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG25
 2 glyco-bond=---- groove=---- planarity=0.602 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG26
 3 glyco-bond=-s-- groove=wn-- planarity=0.507 type=saddle nts=4 GGGG A.DG4,A.DG32,A.DG13,A.DG27

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.DG2,A.DG6,A.DG11,A.DG25
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG26
 3  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG32,A.DG13,A.DG27
  step#1  pm(>>,forward)  area=18.70 rise=3.26 twist=24.5
  step#2  pm(>>,forward)  area=16.65 rise=3.59 twist=27.5
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=--s nts=3 GGG A.DG6,A.DG7,A.DG32
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG25,A.DG26,A.DG27

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG25
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG26
step#1 pm(>>,forward) area=18.70 rise=3.26 twist=24.5

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG26
3 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG32,A.DG13,A.DG27
step#2 pm(>>,forward) area=16.65 rise=3.59 twist=27.5

Download PDB file
Interactive view in 3Dmol.js

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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG25
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG26
  step#1  pm(>>,forward)  area=18.70 rise=3.26 twist=24.5
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG2,A.DG3
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG6,A.DG7
  strand#3  U DNA glyco-bond=-- nts=2 GG A.DG11,A.DG12
  strand#4  U DNA glyco-bond=-- nts=2 GG A.DG25,A.DG26
  loop#1 type=propeller strands=[#1,#2] nts=2 GC A.DG4,A.DC5
  loop#2 type=propeller strands=[#2,#3] nts=3 TTT A.DT8,A.DT9,A.DT10
  loop#3 type=propeller strands=[#3,#4] nts=12 GAAGAGGGAAGA A.DG13,A.DA14,A.DA15,A.DG16,A.DA17,A.DG18,A.DG19,A.DG20,A.DA21,A.DA22,A.DG23,A.DA24

Download PDB file
Interactive view in 3Dmol.js

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

List of 1 non-stem G4-loop (including the two closing Gs)

 1 type=diagonal  helix=#1 nts=6 GGGAGG A.DG27,A.DG28,A.DG29,A.DA30,A.DG31,A.DG32