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

PDB-id
6kfl
Class
DNA
Method
X-ray (1.92 Å)
Summary
Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin tmpyp4
Reference
Zhang, Y.S., Parkinson, G.N., Wei, D.G.: "Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4." To be published
Abstract
 
G4 notes
4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · (2+2), UDUD; parallel(4+0), UUUU · coaxial interfaces: mixed

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

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s-s- groove=wnwn planarity=0.061 type=planar nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 2 glyco-bond=-s-s groove=wnwn planarity=0.202 type=other  nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
 3 glyco-bond=---- groove=---- planarity=0.092 type=planar nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12
 4 glyco-bond=---- groove=---- planarity=0.188 type=other  nts=4 GGGG A.DG10,A.DG13,B.DG10,B.DG13

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, 4 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
 2* glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG10,B.DG13,B.DG10,A.DG13
  step#1  mm(<>,outward)  area=17.16 rise=3.49 twist=13.9
  step#2  pm(>>,forward)  area=7.28  rise=3.22 twist=-37.0
  step#3  pm(>>,forward)  area=7.84  rise=3.26 twist=36.3
  strand#1 DNA glyco-bond=-s-- nts=4 GGGG A.DG2,A.DG1,A.DG9,A.DG10
  strand#2 DNA glyco-bond=s--- nts=4 GGGG A.DG6,A.DG7,B.DG12,B.DG13
  strand#3 DNA glyco-bond=-s-- nts=4 GGGG B.DG2,B.DG1,B.DG9,B.DG10
  strand#4 DNA glyco-bond=s--- nts=4 GGGG B.DG6,B.DG7,A.DG12,A.DG13

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3 stacking diagrams
 1  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
2* glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
step#1 mm(<>,outward) area=17.16 rise=3.49 twist=13.9

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 2* glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
3 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12
step#2 pm(>>,forward) area=7.28 rise=3.22 twist=-37.0

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 3  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG A.DG10,B.DG13,B.DG10,A.DG13
step#3 pm(>>,forward) area=7.84 rise=3.26 twist=36.3

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List of 2 G4-stems [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, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
  step#1  mm(<>,outward)  area=17.16 rise=3.49 twist=13.9
  strand#1  U DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s nts=2 GG A.DG7,A.DG6
  strand#3  U DNA glyco-bond=s- nts=2 GG B.DG1,B.DG2
  strand#4  D DNA glyco-bond=-s nts=2 GG B.DG7,B.DG6
  loop#1 type=lateral   strands=[#1,#2] nts=3 CTC A.DC3,A.DT4,A.DC5
  loop#2 type=lateral   strands=[#3,#4] nts=3 CTC B.DC3,B.DT4,B.DC5

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Stem#2, 2 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG10,A.DG13,B.DG10,B.DG13
  step#1  pm(>>,forward)  area=7.84  rise=3.26 twist=36.3
  strand#1  U DNA glyco-bond=-- nts=2 GG A.DG9,A.DG10
  strand#2  U DNA glyco-bond=-- nts=2 GG A.DG12,A.DG13
  strand#3  U DNA glyco-bond=-- nts=2 GG B.DG9,B.DG10
  strand#4  U DNA glyco-bond=-- nts=2 GG B.DG12,B.DG13
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC11
  loop#2 type=propeller strands=[#3,#4] nts=1 C B.DC11

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [mixed]

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