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

PDB-id
6pnk
Class
DNA
Method
X-ray (2.39 Å)
Summary
Crystal structure of the G-quadruplex formed by (gggtt)3ggg in complex with n-methylmesoporphryin ix
Reference
Yatsunyk, L.A., Lin, L.Y.: "Biophysical and X-ray structural characterization of the (GGGTT)3GGG G-quadruplex in complex with N-methylmesoporphryin IX." To be published
Abstract
 
G4 notes
6 G-tetrads, 2 G4 helices, 2 G4 stems · 3(-P-P), parallel(4+0), UUUU; 3(-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 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.074 type=planar nts=4 GGGG A.DG1,A.DG6,A.DG11,A.DG16
 2 glyco-bond=---- groove=---- planarity=0.095 type=planar nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 3 glyco-bond=---- groove=---- planarity=0.295 type=bowl   nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 4 glyco-bond=---- groove=---- planarity=0.061 type=planar nts=4 GGGG B.DG1,B.DG6,B.DG11,B.DG16
 5 glyco-bond=---- groove=---- planarity=0.060 type=planar nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17
 6 glyco-bond=---- groove=---- planarity=0.318 type=bowl   nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18

List of 2 G4-helices [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.DG1,A.DG6,A.DG11,A.DG16
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
  step#1  pm(>>,forward)  area=8.74  rise=3.33 twist=32.6
  step#2  pm(>>,forward)  area=13.41 rise=3.48 twist=25.7
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG16,A.DG17,A.DG18

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG11,A.DG16
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
step#1 pm(>>,forward) area=8.74 rise=3.33 twist=32.6

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
step#2 pm(>>,forward) area=13.41 rise=3.48 twist=25.7

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Helix#2, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG6,B.DG11,B.DG16
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18
  step#1  pm(>>,forward)  area=8.86  rise=3.32 twist=33.3
  step#2  pm(>>,forward)  area=13.05 rise=3.50 twist=24.1
  strand#1 DNA glyco-bond=--- nts=3 GGG B.DG1,B.DG2,B.DG3
  strand#2 DNA glyco-bond=--- nts=3 GGG B.DG6,B.DG7,B.DG8
  strand#3 DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG16,B.DG17,B.DG18

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG6,B.DG11,B.DG16
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17
step#1 pm(>>,forward) area=8.86 rise=3.32 twist=33.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18
step#2 pm(>>,forward) area=13.05 rise=3.50 twist=24.1

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG6,A.DG11,A.DG16
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
  step#1  pm(>>,forward)  area=8.74  rise=3.33 twist=32.6
  step#2  pm(>>,forward)  area=13.41 rise=3.48 twist=25.7
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG16,A.DG17,A.DG18
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT4,A.DT5
  loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT9,A.DT10
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT14,A.DT15

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG6,B.DG11,B.DG16
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18
  step#1  pm(>>,forward)  area=8.86  rise=3.32 twist=33.3
  step#2  pm(>>,forward)  area=13.05 rise=3.50 twist=24.1
  strand#1  U DNA glyco-bond=--- nts=3 GGG B.DG1,B.DG2,B.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG6,B.DG7,B.DG8
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG16,B.DG17,B.DG18
  loop#1 type=propeller strands=[#2,#3] nts=2 TT B.DT9,B.DT10
  loop#2 type=propeller strands=[#3,#4] nts=2 TT B.DT14,B.DT15

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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)