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

PDB-id
5mtg
Class
DNA
Method
NMR
Summary
G-quadruplex formed within promoters of plasmodium falciparum b var genes - form i
Reference
Juribasic Kulcsar, M., Gabelica, V., Plavec, J.: "Stabilizing interactions in long-loop G-quadruplex formed within promoters of Plasmodium falciparum B var genes." To be published
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-PD+Lw), U3D(3+1), UUUD

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=sss- groove=--wn planarity=0.401 type=bowl   nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
 2 glyco-bond=---s groove=--wn planarity=0.132 type=planar nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
 3 glyco-bond=---s groove=--wn planarity=0.155 type=planar nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23

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=sss- groove=--wn Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
 3  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23
  step#1  mm(<>,outward)  area=15.57 rise=3.57 twist=17.1
  step#2  pm(>>,forward)  area=15.05 rise=3.42 twist=23.0
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG10,A.DG11,A.DG12
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG30,A.DG31,A.DG32
  strand#4 DNA glyco-bond=-ss nts=3 GGG A.DG25,A.DG24,A.DG23

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2 stacking diagrams
 1  glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
2 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
step#1 mm(<>,outward) area=15.57 rise=3.57 twist=17.1

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 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
3 glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23
step#2 pm(>>,forward) area=15.05 rise=3.42 twist=23.0

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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, UUUD, anti-parallel, 3(-PD+Lw), U3D(3+1)

 1  glyco-bond=sss- groove=--wn Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
 2  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
 3  glyco-bond=---s groove=--wn WC-->Major nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23
  step#1  mm(<>,outward)  area=15.57 rise=3.57 twist=17.1
  step#2  pm(>>,forward)  area=15.05 rise=3.42 twist=23.0
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=s-- nts=3 GGG A.DG10,A.DG11,A.DG12
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG30,A.DG31,A.DG32
  strand#4  D DNA glyco-bond=-ss nts=3 GGG A.DG25,A.DG24,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=4 TTAA A.DT6,A.DT7,A.DA8,A.DA9
  loop#2 type=diagonal  strands=[#2,#4] nts=10 TATAACTTTA A.DT13,A.DA14,A.DT15,A.DA16,A.DA17,A.DC18,A.DT19,A.DT20,A.DT21,A.DA22
  loop#3 type=lateral   strands=[#4,#3] nts=4 GTTA A.DG26,A.DT27,A.DT28,A.DA29

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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)