DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 1o0k
Class: DNA
Method: X-ray (1.17 Å)
Summary: Structure of the first parallel DNA quadruplex-drug complex
Reference: Clark GR, Pytel PD, Squire CJ, Neidle S (2003): "Structure of the First Parallel DNA Quadruplex-drug Complex." J.Am.Chem.Soc., 125, 4066-4067. doi: 10.1021/ja0297988.
Abstract: The first crystal structure of a drug (daunomycin) bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) has been determined to high resolution. A planar assemblage of three daunomycin molecules stacks onto the 5' end of the G4 column, with the daunosamine substituents occupying three of the four quadruplex grooves. The surface area of the terminal G-quartet in this parallel DNA quadruplex, presently occupied by three daunomycins, is sufficiently large that it could easily accommodate other potential telomerase inhibitors such as substituted porphyrins or telomestatin.
G4 notes: 8 G-tetrads, 2 G4 helices, 2 G4 stems, UUUU, parallel, 4+0

Cartoon-block schematics in six views (download the tarball)

List of 8 G-tetrads

 1 glyco-bond=---- sugar=-3.3 groove=---- planarity=0.151 type=planar -- nts=4 GGGG 1:A.DG1002,1:D.DG1020,1:C.DG1014,1:B.DG1008
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.081 type=planar -- nts=4 GGGG 1:A.DG1003,1:D.DG1021,1:C.DG1015,1:B.DG1009
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.193 type=bowl   -- nts=4 GGGG 1:A.DG1004,1:D.DG1022,1:C.DG1016,1:B.DG1010
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.251 type=bowl   -- nts=4 GGGG 1:A.DG1005,1:D.DG1023,1:C.DG1017,1:B.DG1011
 5 glyco-bond=---- sugar=-3.3 groove=---- planarity=0.151 type=planar -- nts=4 GGGG 2:A.DG1002,2:D.DG1020,2:C.DG1014,2:B.DG1008
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.081 type=planar -- nts=4 GGGG 2:A.DG1003,2:D.DG1021,2:C.DG1015,2:B.DG1009
 7 glyco-bond=---- sugar=---- groove=---- planarity=0.193 type=bowl   -- nts=4 GGGG 2:A.DG1004,2:D.DG1022,2:C.DG1016,2:B.DG1010
 8 glyco-bond=---- sugar=---- groove=---- planarity=0.251 type=bowl   -- nts=4 GGGG 2:A.DG1005,2:D.DG1023,2:C.DG1017,2:B.DG1011

List of 2 G4-helices

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-tetrads, inter-molecular, with 1 stem

	1 glyco-bond=---- sugar=-3.3 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1002,1:D.DG1020,1:C.DG1014,1:B.DG1008 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1003,1:D.DG1021,1:C.DG1015,1:B.DG1009 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1004,1:D.DG1022,1:C.DG1016,1:B.DG1010 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1005,1:D.DG1023,1:C.DG1017,1:B.DG1011 step#1 pm(>>,forward) area=7.34 rise=3.33 twist=35.8 step#2 pm(>>,forward) area=12.68 rise=3.30 twist=26.8 step#3 pm(>>,forward) area=8.95 rise=3.32 twist=30.7 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG1002,1:A.DG1003,1:A.DG1004,1:A.DG1005 strand#2 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:D.DG1020,1:D.DG1021,1:D.DG1022,1:D.DG1023 strand#3 DNA glyco-bond=---- sugar=.--- nts=4 GGGG 1:C.DG1014,1:C.DG1015,1:C.DG1016,1:C.DG1017 strand#4 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:B.DG1008,1:B.DG1009,1:B.DG1010,1:B.DG1011 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=-3.3 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1002,1:D.DG1020,1:C.DG1014,1:B.DG1008 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1003,1:D.DG1021,1:C.DG1015,1:B.DG1009 step#1 pm(>>,forward) area=7.34 rise=3.33 twist=35.8 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1003,1:D.DG1021,1:C.DG1015,1:B.DG1009 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1004,1:D.DG1022,1:C.DG1016,1:B.DG1010 step#2 pm(>>,forward) area=12.68 rise=3.30 twist=26.8 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1004,1:D.DG1022,1:C.DG1016,1:B.DG1010 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1005,1:D.DG1023,1:C.DG1017,1:B.DG1011 step#3 pm(>>,forward) area=8.95 rise=3.32 twist=30.7 Download PDB file Interactive view in 3Dmol.js

Helix#2, 4 G-tetrads, inter-molecular, with 1 stem

	1 glyco-bond=---- sugar=-3.3 groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1002,2:D.DG1020,2:C.DG1014,2:B.DG1008 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1003,2:D.DG1021,2:C.DG1015,2:B.DG1009 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1004,2:D.DG1022,2:C.DG1016,2:B.DG1010 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1005,2:D.DG1023,2:C.DG1017,2:B.DG1011 step#1 pm(>>,forward) area=7.34 rise=3.33 twist=35.8 step#2 pm(>>,forward) area=12.68 rise=3.30 twist=26.8 step#3 pm(>>,forward) area=8.95 rise=3.32 twist=30.7 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG 2:A.DG1002,2:A.DG1003,2:A.DG1004,2:A.DG1005 strand#2 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 2:D.DG1020,2:D.DG1021,2:D.DG1022,2:D.DG1023 strand#3 DNA glyco-bond=---- sugar=.--- nts=4 GGGG 2:C.DG1014,2:C.DG1015,2:C.DG1016,2:C.DG1017 strand#4 DNA glyco-bond=---- sugar=3--- nts=4 GGGG 2:B.DG1008,2:B.DG1009,2:B.DG1010,2:B.DG1011 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=-3.3 groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1002,2:D.DG1020,2:C.DG1014,2:B.DG1008 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1003,2:D.DG1021,2:C.DG1015,2:B.DG1009 step#1 pm(>>,forward) area=7.34 rise=3.33 twist=35.8 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1003,2:D.DG1021,2:C.DG1015,2:B.DG1009 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1004,2:D.DG1022,2:C.DG1016,2:B.DG1010 step#2 pm(>>,forward) area=12.68 rise=3.30 twist=26.8 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1004,2:D.DG1022,2:C.DG1016,2:B.DG1010 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1005,2:D.DG1023,2:C.DG1017,2:B.DG1011 step#3 pm(>>,forward) area=8.95 rise=3.32 twist=30.7 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=-3.3 groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1002,1:D.DG1020,1:C.DG1014,1:B.DG1008
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1003,1:D.DG1021,1:C.DG1015,1:B.DG1009
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1004,1:D.DG1022,1:C.DG1016,1:B.DG1010
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG1005,1:D.DG1023,1:C.DG1017,1:B.DG1011
  step#1  pm(>>,forward)  area=7.34  rise=3.33 twist=35.8
  step#2  pm(>>,forward)  area=12.68 rise=3.30 twist=26.8
  step#3  pm(>>,forward)  area=8.95  rise=3.32 twist=30.7
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG1002,1:A.DG1003,1:A.DG1004,1:A.DG1005
  strand#2  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:D.DG1020,1:D.DG1021,1:D.DG1022,1:D.DG1023
  strand#3  U DNA glyco-bond=---- sugar=.--- nts=4 GGGG 1:C.DG1014,1:C.DG1015,1:C.DG1016,1:C.DG1017
  strand#4  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 1:B.DG1008,1:B.DG1009,1:B.DG1010,1:B.DG1011

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Interactive view in 3Dmol.js

Stem#2, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0

 1  glyco-bond=---- sugar=-3.3 groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1002,2:D.DG1020,2:C.DG1014,2:B.DG1008
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1003,2:D.DG1021,2:C.DG1015,2:B.DG1009
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1004,2:D.DG1022,2:C.DG1016,2:B.DG1010
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 2:A.DG1005,2:D.DG1023,2:C.DG1017,2:B.DG1011
  step#1  pm(>>,forward)  area=7.34  rise=3.33 twist=35.8
  step#2  pm(>>,forward)  area=12.68 rise=3.30 twist=26.8
  step#3  pm(>>,forward)  area=8.95  rise=3.32 twist=30.7
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG 2:A.DG1002,2:A.DG1003,2:A.DG1004,2:A.DG1005
  strand#2  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 2:D.DG1020,2:D.DG1021,2:D.DG1022,2:D.DG1023
  strand#3  U DNA glyco-bond=---- sugar=.--- nts=4 GGGG 2:C.DG1014,2:C.DG1015,2:C.DG1016,2:C.DG1017
  strand#4  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG 2:B.DG1008,2:B.DG1009,2:B.DG1010,2:B.DG1011