DSSR-derived G-quadruplex features in PDB entry 1l1h
Created by Xiang-Jun Lu <xiangjun@x3dna.org>. 3DNA Forum · User Manual · NAR'15 Paper · PyMOL Plugin.
Summary information [schematics · tetrads · helices · stems · costacks · homepage]
- PDB-id
- 1l1h
- Class
- DNA
- Method
- X-ray (1.75 Å)
- Summary
- Crystal structure of the quadruplex DNA-drug complex
- Reference
- Haider, S.M., Parkinson, G.N., Neidle, S.: (2003) "Structure of a G-quadruplex-Ligand Complex." J.Mol.Biol., 326, 117-125.
- Abstract
- Stabilisation of G-quadruplex structures formed from telomeric DNA, by means of quadruplex-selective ligands, is a means of inhibiting the telomerase enzyme from catalysing the synthesis of telomeric DNA repeats. In order to understand the molecular basis of ligand-quadruplex recognition, the crystal structure has been determined of such a complex, at 1.75A resolution. This complex is between a dimeric antiparallel G-quadruplex formed from the Oxytricha nova telomeric DNA sequence d(GGGGTTTTGGGG), and a di-substituted aminoalkylamido acridine compound. The structure shows that the acridine moiety is bound at one end of the stack of G-quartets, within one of the thymine loops. It is held in place by a combination of stacking interactions and specific hydrogen bonds with thymine bases. The stability of the ligand in this binding site has been confirmed by a 2ns molecular dynamics simulation.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDDU
Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]
List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]
1 glyco-bond=s--s groove=w-n- planarity=0.279 type=bowl nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009 2 glyco-bond=-ss- groove=w-n- planarity=0.192 type=other nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010 3 glyco-bond=s--s groove=w-n- planarity=0.171 type=other nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011 4 glyco-bond=-ss- groove=w-n- planarity=0.202 type=other nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012
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, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009 2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010 3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011 4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012 step#1 mm(<>,outward) area=14.83 rise=3.47 twist=16.2 step#2 pp(><,inward) area=19.13 rise=3.60 twist=37.1 step#3 mm(<>,outward) area=12.73 rise=3.42 twist=19.0 strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1001,A.DG1002,A.DG1003,A.DG1004 strand#2 DNA glyco-bond=-s-s nts=4 GGGG B.DG2004,B.DG2003,B.DG2002,B.DG2001 strand#3 DNA glyco-bond=-s-s nts=4 GGGG A.DG1012,A.DG1011,A.DG1010,A.DG1009 strand#4 DNA glyco-bond=s-s- nts=4 GGGG B.DG2009,B.DG2010,B.DG2011,B.DG2012 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009 |
 |
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010 |
 |
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011 |
List of 1 G4-stem [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, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009 2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010 3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011 4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012 step#1 mm(<>,outward) area=14.83 rise=3.47 twist=16.2 step#2 pp(><,inward) area=19.13 rise=3.60 twist=37.1 step#3 mm(<>,outward) area=12.73 rise=3.42 twist=19.0 strand#1 U DNA glyco-bond=s-s- nts=4 GGGG A.DG1001,A.DG1002,A.DG1003,A.DG1004 strand#2 D DNA glyco-bond=-s-s nts=4 GGGG B.DG2004,B.DG2003,B.DG2002,B.DG2001 strand#3 D DNA glyco-bond=-s-s nts=4 GGGG A.DG1012,A.DG1011,A.DG1010,A.DG1009 strand#4 U DNA glyco-bond=s-s- nts=4 GGGG B.DG2009,B.DG2010,B.DG2011,B.DG2012 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT A.DT1005,A.DT1006,A.DT1007,A.DT1008 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT B.DT2005,B.DT2006,B.DT2007,B.DT2008 |