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

PDB-id
6p45
Class
DNA
Method
X-ray (2.34 Å)
Summary
Crystal structure of the G-quadruplex formed by (tgggt)4 in complex with n-methylmesoporphryin ix
Reference
Yatsunyk, L.A., Lin, L.Y., Powell, B.: "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, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 3(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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=0.070 type=planar nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 2 glyco-bond=---- groove=---- planarity=0.171 type=other  nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 3 glyco-bond=---- groove=---- planarity=0.360 type=bowl   nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 4 glyco-bond=---- groove=---- planarity=0.064 type=planar nts=4 GGGG B.DG2,B.DG7,B.DG12,B.DG17
 5 glyco-bond=---- groove=---- planarity=0.171 type=other  nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18
 6 glyco-bond=---- groove=---- planarity=0.372 type=bowl   nts=4 GGGG B.DG4,B.DG9,B.DG14,B.DG19

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG17,B.DG12,B.DG7,B.DG2
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG18,B.DG13,B.DG8,B.DG3
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG19,B.DG14,B.DG9,B.DG4
  step#1  mp(<<,backward) area=9.16  rise=3.47 twist=28.8
  step#2  mp(<<,backward) area=11.41 rise=3.50 twist=28.0
  step#3  mm(<>,outward)  area=27.69 rise=3.36 twist=-9.2
  step#4  pm(>>,forward)  area=11.00 rise=3.44 twist=28.3
  step#5  pm(>>,forward)  area=9.59  rise=3.51 twist=27.5
  strand#1 DNA glyco-bond=------ nts=6 GGGGGG A.DG4,A.DG3,A.DG2,B.DG17,B.DG18,B.DG19
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG A.DG9,A.DG8,A.DG7,B.DG12,B.DG13,B.DG14
  strand#3 DNA glyco-bond=------ nts=6 GGGGGG A.DG14,A.DG13,A.DG12,B.DG7,B.DG8,B.DG9
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG A.DG19,A.DG18,A.DG17,B.DG2,B.DG3,B.DG4

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
step#1 mp(<<,backward) area=9.16 rise=3.47 twist=28.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
step#2 mp(<<,backward) area=11.41 rise=3.50 twist=28.0

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG7,A.DG12,A.DG17
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG17,B.DG12,B.DG7,B.DG2
step#3 mm(<>,outward) area=27.69 rise=3.36 twist=-9.2

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG17,B.DG12,B.DG7,B.DG2
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG18,B.DG13,B.DG8,B.DG3
step#4 pm(>>,forward) area=11.00 rise=3.44 twist=28.3

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG18,B.DG13,B.DG8,B.DG3
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG19,B.DG14,B.DG9,B.DG4
step#5 pm(>>,forward) area=9.59 rise=3.51 twist=27.5

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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.DG2,A.DG7,A.DG12,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
  step#1  pm(>>,forward)  area=11.41 rise=3.50 twist=28.0
  step#2  pm(>>,forward)  area=9.16  rise=3.47 twist=28.8
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG12,A.DG13,A.DG14
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG17,A.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT5,A.DT6
  loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT10,A.DT11
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT15,A.DT16

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Stem#2, 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 B.DG2,B.DG7,B.DG12,B.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG8,B.DG13,B.DG18
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG9,B.DG14,B.DG19
  step#1  pm(>>,forward)  area=11.00 rise=3.44 twist=28.3
  step#2  pm(>>,forward)  area=9.59  rise=3.51 twist=27.5
  strand#1  U DNA glyco-bond=--- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG12,B.DG13,B.DG14
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG17,B.DG18,B.DG19
  loop#1 type=propeller strands=[#1,#2] nts=2 TT B.DT5,B.DT6
  loop#2 type=propeller strands=[#2,#3] nts=2 TT B.DT10,B.DT11
  loop#3 type=propeller strands=[#3,#4] nts=2 TT B.DT15,B.DT16

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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]  [5'/5']

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