Summary information and primary citation

PDB-id
9kcq
Class
DNA binding protein
Method
X-ray (1.77 Å)
Summary
Crystal structure of an ankyrin protein in complex with g-quadruplex
Reference
Ngo KH, Heddi B, Winnerdy FR, Phan AT: "X-ray structure of a G-quadruplex-ankyrin complex."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UDDU, anti-parallel:basket, 2+2, 3(-LwD+Ln)

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

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List of 3 G-tetrads

 1 glyco-bond=-ss- sugar=.3-- groove=w-n- planarity=0.521 type=other  N+ nts=4 GGGG B.DG2,B.DG10,B.DG22,B.DG14
 2 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.266 type=other  N- nts=4 GGGG B.DG3,B.DG9,B.DG21,B.DG15
 3 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.385 type=bowl   N+ nts=4 GGGG B.DG4,B.DG8,B.DG20,B.DG16

List of 1 G4-helix

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=-ss- sugar=.3-- groove=w-n- WC-->Major N+ nts=4 GGGG B.DG2,B.DG10,B.DG22,B.DG14
 2  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG B.DG3,B.DG9,B.DG21,B.DG15
 3  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG B.DG4,B.DG8,B.DG20,B.DG16
  step#1  pp(><,inward)   area=13.38 rise=3.54 twist=28.2
  step#2  mm(<>,outward)  area=15.00 rise=3.48 twist=14.8
  strand#1 DNA glyco-bond=-s- sugar=.-- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2 DNA glyco-bond=s-s sugar=3-- nts=3 GGG B.DG10,B.DG9,B.DG8
  strand#3 DNA glyco-bond=s-s sugar=--- nts=3 GGG B.DG22,B.DG21,B.DG20
  strand#4 DNA glyco-bond=-s- sugar=--- nts=3 GGG B.DG14,B.DG15,B.DG16

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2 stacking diagrams 
 1  glyco-bond=-ss- sugar=.3-- groove=w-n- WC-->Major N+ nts=4 GGGG B.DG2,B.DG10,B.DG22,B.DG14
 2  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG B.DG3,B.DG9,B.DG21,B.DG15
  step#1  pp(><,inward)   area=13.38 rise=3.54 twist=28.2

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 2  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG B.DG3,B.DG9,B.DG21,B.DG15
 3  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG B.DG4,B.DG8,B.DG20,B.DG16
  step#2  mm(<>,outward)  area=15.00 rise=3.48 twist=14.8

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List of 1 G4-stem

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-tetrads, 3 loops, INTRA-molecular, UDDU, anti-parallel:basket, 2+2, 3(-LwD+Ln)
 1  glyco-bond=-ss- sugar=.3-- groove=w-n- WC-->Major N+ nts=4 GGGG B.DG2,B.DG10,B.DG22,B.DG14
 2  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC N- nts=4 GGGG B.DG3,B.DG9,B.DG21,B.DG15
 3  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major N+ nts=4 GGGG B.DG4,B.DG8,B.DG20,B.DG16
  step#1  pp(><,inward)   area=13.38 rise=3.54 twist=28.2
  step#2  mm(<>,outward)  area=15.00 rise=3.48 twist=14.8
  strand#1  U DNA glyco-bond=-s- sugar=.-- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2  D DNA glyco-bond=s-s sugar=3-- nts=3 GGG B.DG10,B.DG9,B.DG8
  strand#3  D DNA glyco-bond=s-s sugar=--- nts=3 GGG B.DG22,B.DG21,B.DG20
  strand#4  U DNA glyco-bond=-s- sugar=--- nts=3 GGG B.DG14,B.DG15,B.DG16
  loop#1 type=lateral   strands=[#1,#2] nts=3 TTA B.DT5,B.DT6,B.DA7
  loop#2 type=diagonal  strands=[#2,#4] nts=3 TTT B.DT11,B.DT12,B.DT13
  loop#3 type=lateral   strands=[#4,#3] nts=3 TTA B.DT17,B.DT18,B.DA19

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