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

PDB-id
4p1d
Class
DNA
Method
X-ray (1.55 Å)
Summary
Structure of the complex of a bimolecular human telomeric DNA with coptisine
Reference
Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R., Sissi, C.: "Crystal Structure of the complex of a bimolecular human telomeric DNA with Coptisine." To be published
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 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=0.138 type=planar nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2 glyco-bond=---- groove=---- planarity=0.136 type=planar nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3 glyco-bond=---- groove=---- planarity=0.264 type=bowl   nts=4 GGGG A.DG5,A.DG11,B.DG17,B.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, inter-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
  step#1  pm(>>,forward)  area=8.61  rise=3.32 twist=32.3
  step#2  pm(>>,forward)  area=12.50 rise=3.43 twist=26.5
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG21,B.DG22,B.DG23

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
step#1 pm(>>,forward) area=8.61 rise=3.32 twist=32.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
step#2 pm(>>,forward) area=12.50 rise=3.43 twist=26.5

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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, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
  step#1  pm(>>,forward)  area=8.61  rise=3.32 twist=32.3
  step#2  pm(>>,forward)  area=12.50 rise=3.43 twist=26.5
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG21,B.DG22,B.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8
  loop#2 type=propeller strands=[#3,#4] nts=3 TTA B.DT18,B.DT19,B.DA20

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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)