Summary information

PDB id
1hao
Class
hydrolase-hydrolase inhibitor-DNA
Method
X-ray (2.8 Å)
Summary
Complex of human alpha-thrombin with a 15mer oligonucleotide ggttggtgtggttgg (based on NMR model of DNA)
Reference
Padmanabhan K, Tulinsky A (1996): "An ambiguous structure of a DNA 15-mer thrombin complex." Acta Crystallogr.,Sect.D, 52, 272-282. doi: 10.1107/S0907444995013977.
Abstract
The structure of a complex between thrombin and a GGTTGGTGTGGTTGG DNA 15-mer has been analyzed crystallographically. The solution NMR structure of the 15-mer has two stacked G-quartets similar to that found in the previous X-ray structure determination of the 15-mer-thrombin complex [Padmanabhan, Padmanabhan, Ferrara, Sadler & Tulinsky (1993). J. Biol. Chem. 268, 17651-17654]; the strand polarity, however, is reversed from that of the crystallographic structure. The structure of the complex here has been redetermined with better diffraction data confirming the previous crystallographic structure but also indicating that the NMR solution structure fits equally well. Both 15-mer complex structures refined to an R value of about 0.16 presenting a disconcerting ambiguity. Since the two 15-mer structures associate with thrombin in different ways (through the TGT loop in the X-ray and TT loop in the NMR model), other independent lines of physical or chemical evidence are required to resolve the ambiguity.
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=---3 groove=wnwn planarity=0.373 type=other  nts=4 GGGG D.DG401,D.DG415,D.DG410,D.DG406
 2 glyco-bond=-s-s sugar=---. groove=wnwn planarity=0.441 type=other  nts=4 GGGG D.DG402,D.DG414,D.DG411,D.DG405

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---3 groove=wnwn Major-->WC nts=4 GGGG D.DG401,D.DG415,D.DG410,D.DG406
 2  glyco-bond=-s-s sugar=---. groove=wnwn WC-->Major nts=4 GGGG D.DG402,D.DG414,D.DG411,D.DG405
  step#1  mm(<>,outward)  area=19.52 rise=3.70 twist=12.0
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG D.DG401,D.DG402
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG D.DG415,D.DG414
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG D.DG410,D.DG411
  strand#4 DNA glyco-bond=-s sugar=3. nts=2 GG D.DG406,D.DG405

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1 stacking diagram 
 1  glyco-bond=s-s- sugar=---3 groove=wnwn Major-->WC nts=4 GGGG D.DG401,D.DG415,D.DG410,D.DG406
 2  glyco-bond=-s-s sugar=---. groove=wnwn WC-->Major nts=4 GGGG D.DG402,D.DG414,D.DG411,D.DG405
  step#1  mm(<>,outward)  area=19.52 rise=3.70 twist=12.0

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 2(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---3 groove=wnwn Major-->WC nts=4 GGGG D.DG401,D.DG415,D.DG410,D.DG406
 2  glyco-bond=-s-s sugar=---. groove=wnwn WC-->Major nts=4 GGGG D.DG402,D.DG414,D.DG411,D.DG405
  step#1  mm(<>,outward)  area=19.52 rise=3.70 twist=12.0
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG401,D.DG402
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG D.DG415,D.DG414
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG D.DG410,D.DG411
  strand#4  D DNA glyco-bond=-s sugar=3. nts=2 GG D.DG406,D.DG405
  loop#1 type=lateral   strands=[#1,#4] nts=2 TT D.DT403,D.DT404
  loop#2 type=lateral   strands=[#4,#3] nts=3 TGT D.DT407,D.DG408,D.DT409
  loop#3 type=lateral   strands=[#3,#2] nts=2 TT D.DT412,D.DT413

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