Detailed DSSR results for the G-quadruplex: PDB entry 2gwq
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 2gwq
- Class
- DNA
- Method
- X-ray (2.0 Å)
- Summary
- Crystal structure of d(g4t4g4) with four quadruplexes in the asymmetric unit.
- Reference
- Lee MPH, Haider S, Parkinson GN, Neidle S: "Crystal structure of D(G4T4G4) with four and six quadruplexes in the asymmetric unit."
- Abstract
- G4 notes
- 16 G-tetrads, 4 G4 helices, 4 G4 stems, (2+2), UDDU
Base-block schematics in six views
List of 16 G-tetrads
1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.255 type=bowl nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.116 type=planar nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.112 type=planar nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.240 type=other nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 5 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.244 type=other nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 6 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.098 type=planar nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 7 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.094 type=planar nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 8 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.271 type=bowl nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48 9 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.234 type=other nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69 10 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.118 type=planar nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70 11 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.119 type=planar nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71 12 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.235 type=bowl nts=4 GGGG E.DG52,F.DG61,E.DG57,F.DG72 13 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.288 type=bowl nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93 14 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.102 type=planar nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94 15 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.127 type=planar nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95 16 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.245 type=other nts=4 GGGG G.DG76,H.DG85,G.DG81,H.DG96
List of 4 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-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 step#1 mm(<>,outward) area=14.33 rise=3.49 twist=17.3 step#2 pp(><,inward) area=20.17 rise=3.56 twist=36.5 step#3 mm(<>,outward) area=13.64 rise=3.46 twist=17.9 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 |
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2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 |
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3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 |
Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48 step#1 mm(<>,outward) area=12.90 rise=3.52 twist=18.0 step#2 pp(><,inward) area=19.52 rise=3.52 twist=36.7 step#3 mm(<>,outward) area=13.25 rise=3.44 twist=17.7 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 |
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2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 |
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3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 |
Helix#3, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG E.DG52,F.DG61,E.DG57,F.DG72 step#1 mm(<>,outward) area=13.14 rise=3.49 twist=17.5 step#2 pp(><,inward) area=20.49 rise=3.55 twist=37.0 step#3 mm(<>,outward) area=13.57 rise=3.45 twist=17.8 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG E.DG49,E.DG50,E.DG51,E.DG52 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG F.DG64,F.DG63,F.DG62,F.DG61 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG E.DG60,E.DG59,E.DG58,E.DG57 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG F.DG69,F.DG70,F.DG71,F.DG72 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69 |
 |
2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70 |
 |
3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71 |
Helix#4, 4 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG76,H.DG85,G.DG81,H.DG96 step#1 mm(<>,outward) area=14.40 rise=3.50 twist=16.9 step#2 pp(><,inward) area=19.23 rise=3.55 twist=36.8 step#3 mm(<>,outward) area=13.48 rise=3.46 twist=18.0 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG G.DG73,G.DG74,G.DG75,G.DG76 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG H.DG88,H.DG87,H.DG86,H.DG85 strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG G.DG84,G.DG83,G.DG82,G.DG81 strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG H.DG93,H.DG94,H.DG95,H.DG96 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93 |
 |
2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94 |
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3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95 |
List of 4 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-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 step#1 mm(<>,outward) area=14.33 rise=3.49 twist=17.3 step#2 pp(><,inward) area=20.17 rise=3.56 twist=36.5 step#3 mm(<>,outward) area=13.64 rise=3.46 twist=17.9 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT B.DT17,B.DT18,B.DT19,B.DT20 |
Stem#2, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48 step#1 mm(<>,outward) area=12.90 rise=3.52 twist=18.0 step#2 pp(><,inward) area=19.52 rise=3.52 twist=36.7 step#3 mm(<>,outward) area=13.25 rise=3.44 twist=17.7 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT C.DT29,C.DT30,C.DT31,C.DT32 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT D.DT41,D.DT42,D.DT43,D.DT44 |
Stem#3, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG E.DG49,F.DG64,E.DG60,F.DG69 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG E.DG50,F.DG63,E.DG59,F.DG70 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG E.DG51,F.DG62,E.DG58,F.DG71 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG E.DG52,F.DG61,E.DG57,F.DG72 step#1 mm(<>,outward) area=13.14 rise=3.49 twist=17.5 step#2 pp(><,inward) area=20.49 rise=3.55 twist=37.0 step#3 mm(<>,outward) area=13.57 rise=3.45 twist=17.8 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG E.DG49,E.DG50,E.DG51,E.DG52 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG F.DG64,F.DG63,F.DG62,F.DG61 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG E.DG60,E.DG59,E.DG58,E.DG57 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG F.DG69,F.DG70,F.DG71,F.DG72 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT E.DT53,E.DT54,E.DT55,E.DT56 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT F.DT65,F.DT66,F.DT67,F.DT68 |
Stem#4, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG73,H.DG88,G.DG84,H.DG93 2 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG74,H.DG87,G.DG83,H.DG94 3 glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG75,H.DG86,G.DG82,H.DG95 4 glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG76,H.DG85,G.DG81,H.DG96 step#1 mm(<>,outward) area=14.40 rise=3.50 twist=16.9 step#2 pp(><,inward) area=19.23 rise=3.55 twist=36.8 step#3 mm(<>,outward) area=13.48 rise=3.46 twist=18.0 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG G.DG73,G.DG74,G.DG75,G.DG76 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG H.DG88,H.DG87,H.DG86,H.DG85 strand#3 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG G.DG84,G.DG83,G.DG82,G.DG81 strand#4 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG H.DG93,H.DG94,H.DG95,H.DG96 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT G.DT77,G.DT78,G.DT79,G.DT80 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT H.DT89,H.DT90,H.DT91,H.DT92 |