DSSR-enabled G4 identification/annotation

Summary information and primary citation

PDB-id: 9fta
Class: DNA
Method: X-ray (2.49 Å)
Summary: Crystal structure of d(ggggttttgggg) with zn and k
Reference: Sbirkova-Dimitrova HI, Shivachev BL: "Crystal structure of d(GGGGTTTTGGGG) with Zn and K."
Abstract
G4 notes: 8 G-tetrads, 2 G4 helices, 2 G4 stems, UDDU, anti-parallel:basket, 2+2

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

List of 8 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.219 type=other  -- nts=4 GGGG 1:AAA.DG1001,1:BBB.DG2004,1:AAA.DG1012,1:BBB.DG2009
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.168 type=other  -- nts=4 GGGG 1:AAA.DG1002,1:BBB.DG2003,1:AAA.DG1011,1:BBB.DG2010
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.149 type=planar -- nts=4 GGGG 1:AAA.DG1003,1:BBB.DG2002,1:AAA.DG1010,1:BBB.DG2011
 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.218 type=other  -- nts=4 GGGG 1:AAA.DG1004,1:BBB.DG2001,1:AAA.DG1009,1:BBB.DG2012
 5 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.165 type=other  -- nts=4 GGGG 1:CCC.DG1001,1:DDD.DG2004,1:CCC.DG1012,1:DDD.DG2009
 6 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.186 type=other  -- nts=4 GGGG 1:CCC.DG1002,1:DDD.DG2003,1:CCC.DG1011,1:DDD.DG2010
 7 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.190 type=other  -- nts=4 GGGG 1:CCC.DG1003,1:DDD.DG2002,1:CCC.DG1010,1:DDD.DG2011
 8 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.297 type=bowl   -- nts=4 GGGG 1:CCC.DG1004,1:DDD.DG2001,1:CCC.DG1009,1:DDD.DG2012

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=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:AAA.DG1001,1:BBB.DG2004,1:AAA.DG1012,1:BBB.DG2009 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:AAA.DG1002,1:BBB.DG2003,1:AAA.DG1011,1:BBB.DG2010 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:AAA.DG1003,1:BBB.DG2002,1:AAA.DG1010,1:BBB.DG2011 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:AAA.DG1004,1:BBB.DG2001,1:AAA.DG1009,1:BBB.DG2012 step#1 mm(<>,outward) area=12.01 rise=3.54 twist=18.1 step#2 pp(><,inward) area=22.17 rise=3.51 twist=35.8 step#3 mm(<>,outward) area=12.68 rise=3.49 twist=17.7 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:AAA.DG1001,1:AAA.DG1002,1:AAA.DG1003,1:AAA.DG1004 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:BBB.DG2004,1:BBB.DG2003,1:BBB.DG2002,1:BBB.DG2001 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:AAA.DG1012,1:AAA.DG1011,1:AAA.DG1010,1:AAA.DG1009 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:BBB.DG2009,1:BBB.DG2010,1:BBB.DG2011,1:BBB.DG2012 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:AAA.DG1001,1:BBB.DG2004,1:AAA.DG1012,1:BBB.DG2009 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:AAA.DG1002,1:BBB.DG2003,1:AAA.DG1011,1:BBB.DG2010 step#1 mm(<>,outward) area=12.01 rise=3.54 twist=18.1 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:AAA.DG1002,1:BBB.DG2003,1:AAA.DG1011,1:BBB.DG2010 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:AAA.DG1003,1:BBB.DG2002,1:AAA.DG1010,1:BBB.DG2011 step#2 pp(><,inward) area=22.17 rise=3.51 twist=35.8 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:AAA.DG1003,1:BBB.DG2002,1:AAA.DG1010,1:BBB.DG2011 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:AAA.DG1004,1:BBB.DG2001,1:AAA.DG1009,1:BBB.DG2012 step#3 mm(<>,outward) area=12.68 rise=3.49 twist=17.7 Download PDB file Interactive view in 3Dmol.js

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

	1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:CCC.DG1001,1:DDD.DG2004,1:CCC.DG1012,1:DDD.DG2009 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:CCC.DG1002,1:DDD.DG2003,1:CCC.DG1011,1:DDD.DG2010 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:CCC.DG1003,1:DDD.DG2002,1:CCC.DG1010,1:DDD.DG2011 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:CCC.DG1004,1:DDD.DG2001,1:CCC.DG1009,1:DDD.DG2012 step#1 mm(<>,outward) area=14.18 rise=3.48 twist=17.2 step#2 pp(><,inward) area=20.46 rise=3.52 twist=36.5 step#3 mm(<>,outward) area=12.95 rise=3.50 twist=17.4 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:CCC.DG1001,1:CCC.DG1002,1:CCC.DG1003,1:CCC.DG1004 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:DDD.DG2004,1:DDD.DG2003,1:DDD.DG2002,1:DDD.DG2001 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:CCC.DG1012,1:CCC.DG1011,1:CCC.DG1010,1:CCC.DG1009 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:DDD.DG2009,1:DDD.DG2010,1:DDD.DG2011,1:DDD.DG2012 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:CCC.DG1001,1:DDD.DG2004,1:CCC.DG1012,1:DDD.DG2009 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:CCC.DG1002,1:DDD.DG2003,1:CCC.DG1011,1:DDD.DG2010 step#1 mm(<>,outward) area=14.18 rise=3.48 twist=17.2 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:CCC.DG1002,1:DDD.DG2003,1:CCC.DG1011,1:DDD.DG2010 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:CCC.DG1003,1:DDD.DG2002,1:CCC.DG1010,1:DDD.DG2011 step#2 pp(><,inward) area=20.46 rise=3.52 twist=36.5 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:CCC.DG1003,1:DDD.DG2002,1:CCC.DG1010,1:DDD.DG2011 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:CCC.DG1004,1:DDD.DG2001,1:CCC.DG1009,1:DDD.DG2012 step#3 mm(<>,outward) area=12.95 rise=3.50 twist=17.4 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, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:AAA.DG1001,1:BBB.DG2004,1:AAA.DG1012,1:BBB.DG2009
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:AAA.DG1002,1:BBB.DG2003,1:AAA.DG1011,1:BBB.DG2010
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:AAA.DG1003,1:BBB.DG2002,1:AAA.DG1010,1:BBB.DG2011
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:AAA.DG1004,1:BBB.DG2001,1:AAA.DG1009,1:BBB.DG2012
  step#1  mm(<>,outward)  area=12.01 rise=3.54 twist=18.1
  step#2  pp(><,inward)   area=22.17 rise=3.51 twist=35.8
  step#3  mm(<>,outward)  area=12.68 rise=3.49 twist=17.7
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:AAA.DG1001,1:AAA.DG1002,1:AAA.DG1003,1:AAA.DG1004
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:BBB.DG2004,1:BBB.DG2003,1:BBB.DG2002,1:BBB.DG2001
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:AAA.DG1012,1:AAA.DG1011,1:AAA.DG1010,1:AAA.DG1009
  strand#4  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:BBB.DG2009,1:BBB.DG2010,1:BBB.DG2011,1:BBB.DG2012
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT 1:AAA.DT1005,1:AAA.DT1006,1:AAA.DT1007,1:AAA.DT1008
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT 1:BBB.DT2005,1:BBB.DT2006,1:BBB.DT2007,1:BBB.DT2008

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Interactive view in 3Dmol.js

Stem#2, 4 G-tetrads, 2 loops, inter-molecular, UDDU, anti-parallel:basket, 2+2

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:CCC.DG1001,1:DDD.DG2004,1:CCC.DG1012,1:DDD.DG2009
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:CCC.DG1002,1:DDD.DG2003,1:CCC.DG1011,1:DDD.DG2010
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC -- nts=4 GGGG 1:CCC.DG1003,1:DDD.DG2002,1:CCC.DG1010,1:DDD.DG2011
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major -- nts=4 GGGG 1:CCC.DG1004,1:DDD.DG2001,1:CCC.DG1009,1:DDD.DG2012
  step#1  mm(<>,outward)  area=14.18 rise=3.48 twist=17.2
  step#2  pp(><,inward)   area=20.46 rise=3.52 twist=36.5
  step#3  mm(<>,outward)  area=12.95 rise=3.50 twist=17.4
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:CCC.DG1001,1:CCC.DG1002,1:CCC.DG1003,1:CCC.DG1004
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:DDD.DG2004,1:DDD.DG2003,1:DDD.DG2002,1:DDD.DG2001
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG 1:CCC.DG1012,1:CCC.DG1011,1:CCC.DG1010,1:CCC.DG1009
  strand#4  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG 1:DDD.DG2009,1:DDD.DG2010,1:DDD.DG2011,1:DDD.DG2012
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT 1:CCC.DT1005,1:CCC.DT1006,1:CCC.DT1007,1:CCC.DT1008
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT 1:DDD.DT2005,1:DDD.DT2006,1:DDD.DT2007,1:DDD.DT2008