Detailed DSSR results for the G-quadruplex: PDB entry 8u5t
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
- 8u5t
- Class
- RNA
- Method
- X-ray (2.2 Å)
- Summary
- Structure of mango ii variant aptamer bound to t01-6a-b
- Reference
- Passalacqua LFM, Ferre-D'Amare AR: "Structure of Mango II variant aptamer bound to T01-6A-B."
- Abstract
- G4 notes
- 9 G-tetrads, 2 G4 helices, 3 G4 stems, 1 G4 coaxial stack, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'
Base-block schematics in six views
List of 9 G-tetrads
1 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.264 type=bowl-2 nts=4 GGGG A.G10,A.G15,A.G20,A.G25 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.159 type=planar nts=4 GGGG A.G11,A.G16,A.G21,A.G26 3 glyco-bond=---- sugar=---- groove=---- planarity=0.120 type=planar nts=4 GGGG A.G13,A.G29,A.G23,A.G18 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.309 type=other nts=4 GGGG B.G10,B.G15,B.G20,B.G25 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.140 type=planar nts=4 GGGG B.G11,B.G16,B.G21,B.G26 6 glyco-bond=---- sugar=---- groove=---- planarity=0.105 type=planar nts=4 GGGG B.G13,B.G29,B.G23,B.G18 7 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.289 type=bowl-2 nts=4 GGGG C.G10,C.G15,C.G20,C.G25 8 glyco-bond=---- sugar=3333 groove=---- planarity=0.103 type=planar nts=4 GGGG C.G11,C.G16,C.G21,C.G26 9 glyco-bond=---- sugar=---- groove=---- planarity=0.053 type=planar nts=4 GGGG C.G13,C.G29,C.G23,C.G18
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, 3 G-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G10,A.G15,A.G20,A.G25 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G11,A.G16,A.G21,A.G26 3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.G13,A.G18,A.G23,A.G29 step#1 pm(>>,forward) area=8.56 rise=3.31 twist=34.1 step#2 pp(><,inward) area=27.66 rise=3.37 twist=28.1 strand#1 RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G10,A.G11,A.G13 strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG A.G15,A.G16,A.G18 strand#3 RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G20,A.G21,A.G23 strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG A.G25,A.G26,A.G29 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G10,A.G15,A.G20,A.G25 |
 |
2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G11,A.G16,A.G21,A.G26 |
Helix#2, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.G13,B.G29,B.G23,B.G18 2 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G11,B.G26,B.G21,B.G16 3* glyco-bond=---- sugar=-3-3 groove=---- Major-->WC nts=4 GGGG B.G10,B.G25,B.G20,B.G15 4 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG C.G15,C.G20,C.G25,C.G10 5 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG C.G16,C.G21,C.G26,C.G11 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG C.G18,C.G23,C.G29,C.G13 step#1 pp(><,inward) area=27.82 rise=3.35 twist=27.9 step#2 mp(<<,backward) area=8.36 rise=3.30 twist=33.9 step#3 mm(<>,outward) area=19.79 rise=3.62 twist=10.7 step#4 pm(>>,forward) area=8.33 rise=3.28 twist=34.1 step#5 pp(><,inward) area=27.78 rise=3.34 twist=27.8 strand#1 RNA glyco-bond=------ sugar=-3-33- nts=6 GGGGGG B.G13,B.G11,B.G10,C.G15,C.G16,C.G18 strand#2 RNA glyco-bond=------ sugar=-33-3- nts=6 GGGGGG B.G29,B.G26,B.G25,C.G20,C.G21,C.G23 strand#3 RNA glyco-bond=------ sugar=-3-33- nts=6 GGGGGG B.G23,B.G21,B.G20,C.G25,C.G26,C.G29 strand#4 RNA glyco-bond=------ sugar=-33-3- nts=6 GGGGGG B.G18,B.G16,B.G15,C.G10,C.G11,C.G13 |
| 5 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.G13,B.G29,B.G23,B.G18 |
 |
2 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G11,B.G26,B.G21,B.G16 |
 |
3* glyco-bond=---- sugar=-3-3 groove=---- Major-->WC nts=4 GGGG B.G10,B.G25,B.G20,B.G15 |
 |
4 glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG C.G15,C.G20,C.G25,C.G10 |
 |
5 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG C.G16,C.G21,C.G26,C.G11 |
List of 3 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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G10,A.G15,A.G20,A.G25 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G11,A.G16,A.G21,A.G26 step#1 pm(>>,forward) area=8.56 rise=3.31 twist=34.1 strand#1 U RNA glyco-bond=-- sugar=-3 nts=2 GG A.G10,A.G11 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG A.G15,A.G16 strand#3 U RNA glyco-bond=-- sugar=-3 nts=2 GG A.G20,A.G21 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG A.G25,A.G26 loop#1 type=propeller strands=[#1,#2] nts=3 UGA A.U12,A.G13,A.A14 loop#2 type=propeller strands=[#2,#3] nts=3 AGA A.A17,A.G18,A.A19 loop#3 type=propeller strands=[#3,#4] nts=3 CGA A.C22,A.G23,A.A24 |
Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG B.G10,B.G15,B.G20,B.G25 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G11,B.G16,B.G21,B.G26 step#1 pm(>>,forward) area=8.36 rise=3.30 twist=33.9 strand#1 U RNA glyco-bond=-- sugar=-3 nts=2 GG B.G10,B.G11 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG B.G15,B.G16 strand#3 U RNA glyco-bond=-- sugar=-3 nts=2 GG B.G20,B.G21 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG B.G25,B.G26 loop#1 type=propeller strands=[#1,#2] nts=3 UGA B.U12,B.G13,B.A14 loop#2 type=propeller strands=[#2,#3] nts=3 AGA B.A17,B.G18,B.A19 loop#3 type=propeller strands=[#3,#4] nts=3 CGA B.C22,B.G23,B.A24 |
Stem#3, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG C.G10,C.G15,C.G20,C.G25 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG C.G11,C.G16,C.G21,C.G26 step#1 pm(>>,forward) area=8.33 rise=3.28 twist=34.1 strand#1 U RNA glyco-bond=-- sugar=-3 nts=2 GG C.G10,C.G11 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG C.G15,C.G16 strand#3 U RNA glyco-bond=-- sugar=-3 nts=2 GG C.G20,C.G21 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG C.G25,C.G26 loop#1 type=propeller strands=[#1,#2] nts=3 UGA C.U12,C.G13,C.A14 loop#2 type=propeller strands=[#2,#3] nts=3 AGA C.A17,C.G18,C.A19 loop#3 type=propeller strands=[#3,#4] nts=3 CGA C.C22,C.G23,C.A24 |
List of 1 G4 coaxial stack
1 G4 helix#2 contains 2 G4 stems: [#2,#3] [5'/5']