DSSR-enabled G4 identification/annotation: PDB entry 8vxx
Summary information and primary citation
- PDB-id
- 8vxx
- Class
- RNA
- Method
- X-ray (3.1 Å)
- Summary
- Mango ii bound to 365a-061
- Reference
- Passalacqua LFM, Ferre-D'Amare AR, Schneekloth JS: "Mango II bound to 365A-061."
- Abstract
- G4 notes
- 9 G-tetrads, 2 G4 helices, 3 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 3(-P-P-P), coaxial interfaces: 5'/5'
Cartoon-block schematics in six views (download the tarball)
List of 9 G-tetrads
1 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.263 type=other O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.166 type=other O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- planarity=0.122 type=planar O- nts=4 GGGG 1:A.G13,1:A.G29,1:A.G24,1:A.G18 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.345 type=other O+ nts=4 GGGG 1:B.G10,1:B.G15,1:B.G20,1:B.G26 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.156 type=planar O+ nts=4 GGGG 1:B.G11,1:B.G16,1:B.G21,1:B.G27 6 glyco-bond=---- sugar=---- groove=---- planarity=0.176 type=other O- nts=4 GGGG 1:B.G13,1:B.G29,1:B.G24,1:B.G18 7 glyco-bond=---- sugar=33-3 groove=---- planarity=0.289 type=other O+ nts=4 GGGG 1:C.G10,1:C.G15,1:C.G20,1:C.G26 8 glyco-bond=---- sugar=3333 groove=---- planarity=0.101 type=planar O+ nts=4 GGGG 1:C.G11,1:C.G16,1:C.G21,1:C.G27 9 glyco-bond=---- sugar=---- groove=---- planarity=0.181 type=other O- nts=4 GGGG 1:C.G13,1:C.G29,1:C.G24,1: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-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G24,1:A.G29 step#1 pm(>>,forward) area=8.89 rise=3.27 twist=35.3 step#2 pp(><,inward) area=27.32 rise=3.30 twist=27.8 strand#1 RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G10,1:A.G11,1:A.G13 strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G15,1:A.G16,1:A.G18 strand#3 RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G20,1:A.G21,1:A.G24 strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G26,1:A.G27,1:A.G29 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 |
|
2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 |
Helix#2, 6 G-tetrads, inter-molecular, with 2 stems
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O- nts=4 GGGG 1:B.G13,1:B.G29,1:B.G24,1:B.G18 2 glyco-bond=---- sugar=3333 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G11,1:B.G27,1:B.G21,1:B.G16 3* glyco-bond=---- sugar=-3-3 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G10,1:B.G26,1:B.G20,1:B.G15 4 glyco-bond=---- sugar=3-33 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G15,1:C.G20,1:C.G26,1:C.G10 5 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G16,1:C.G21,1:C.G27,1:C.G11 6 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:C.G18,1:C.G24,1:C.G29,1:C.G13 step#1 pp(><,inward) area=29.67 rise=3.34 twist=26.5 step#2 mp(<<,backward) area=7.53 rise=3.31 twist=36.1 step#3 mm(<>,outward) area=20.00 rise=3.56 twist=8.4 step#4 pm(>>,forward) area=6.92 rise=3.32 twist=36.3 step#5 pp(><,inward) area=29.58 rise=3.35 twist=27.2 strand#1 RNA glyco-bond=------ sugar=-3-33- nts=6 GGGGGG 1:B.G13,1:B.G11,1:B.G10,1:C.G15,1:C.G16,1:C.G18 strand#2 RNA glyco-bond=------ sugar=-33-3- nts=6 GGGGGG 1:B.G29,1:B.G27,1:B.G26,1:C.G20,1:C.G21,1:C.G24 strand#3 RNA glyco-bond=------ sugar=-3-33- nts=6 GGGGGG 1:B.G24,1:B.G21,1:B.G20,1:C.G26,1:C.G27,1:C.G29 strand#4 RNA glyco-bond=------ sugar=-3333- nts=6 GGGGGG 1:B.G18,1:B.G16,1:B.G15,1:C.G10,1:C.G11,1:C.G13 |
| 5 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O- nts=4 GGGG 1:B.G13,1:B.G29,1:B.G24,1:B.G18 |
|
2 glyco-bond=---- sugar=3333 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G11,1:B.G27,1:B.G21,1:B.G16 |
|
3* glyco-bond=---- sugar=-3-3 groove=---- Major-->WC O+ nts=4 GGGG 1:B.G10,1:B.G26,1:B.G20,1:B.G15 |
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4 glyco-bond=---- sugar=3-33 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G15,1:C.G20,1:C.G26,1:C.G10 |
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5 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G16,1:C.G21,1:C.G27,1: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, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
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1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G24,1:A.G29 step#1 pm(>>,forward) area=8.89 rise=3.27 twist=35.3 step#2 pp(><,inward) area=27.32 rise=3.30 twist=27.8 strand#1* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G10,1:A.G11,1:A.G13 bulged-nts=1 A 1:A.A12 strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G15,1:A.G16,1:A.G18 bulged-nts=1 A 1:A.A17 strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G20,1:A.G21,1:A.G24 bulged-nts=2 AA 1:A.A22,1:A.A23 strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G26,1:A.G27,1:A.G29 bulged-nts=1 A 1:A.A28 loop#1 type=propeller strands=[#1,#2] nts=1 A 1:A.A14 loop#2 type=propeller strands=[#2,#3] nts=1 A 1:A.A19 loop#3 type=propeller strands=[#3,#4] nts=1 A 1:A.A25 |
Stem#2, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
|
1 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 GGGG 1:B.G10,1:B.G15,1:B.G20,1:B.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:B.G11,1:B.G16,1:B.G21,1:B.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:B.G13,1:B.G18,1:B.G24,1:B.G29 step#1 pm(>>,forward) area=7.53 rise=3.31 twist=36.1 step#2 pp(><,inward) area=29.67 rise=3.34 twist=26.5 strand#1* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:B.G10,1:B.G11,1:B.G13 bulged-nts=1 A 1:B.A12 strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:B.G15,1:B.G16,1:B.G18 bulged-nts=1 A 1:B.A17 strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:B.G20,1:B.G21,1:B.G24 bulged-nts=2 AA 1:B.A22,1:B.A23 strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:B.G26,1:B.G27,1:B.G29 bulged-nts=1 A 1:B.A28 loop#1 type=propeller strands=[#1,#2] nts=1 A 1:B.A14 loop#2 type=propeller strands=[#2,#3] nts=1 A 1:B.A19 loop#3 type=propeller strands=[#3,#4] nts=1 A 1:B.A25 |
Stem#3, 3 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
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1 glyco-bond=---- sugar=33-3 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G10,1:C.G15,1:C.G20,1:C.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:C.G11,1:C.G16,1:C.G21,1:C.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:C.G13,1:C.G18,1:C.G24,1:C.G29 step#1 pm(>>,forward) area=6.92 rise=3.32 twist=36.3 step#2 pp(><,inward) area=29.58 rise=3.35 twist=27.2 strand#1* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:C.G10,1:C.G11,1:C.G13 bulged-nts=1 A 1:C.A12 strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:C.G15,1:C.G16,1:C.G18 bulged-nts=1 A 1:C.A17 strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:C.G20,1:C.G21,1:C.G24 bulged-nts=2 AA 1:C.A22,1:C.A23 strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:C.G26,1:C.G27,1:C.G29 bulged-nts=1 A 1:C.A28 loop#1 type=propeller strands=[#1,#2] nts=1 A 1:C.A14 loop#2 type=propeller strands=[#2,#3] nts=1 A 1:C.A19 loop#3 type=propeller strands=[#3,#4] nts=1 A 1:C.A25 |
List of 1 G4 coaxial stack
1 G4 helix#2 contains 2 G4 stems: [#2,#3] [5'/5']