DSSR-enabled G4 identification/annotation: PDB entry 9p3a
Summary information and primary citation
- PDB-id
- 9p3a
- Class
- DNA
- Method
- X-ray (2.34 Å)
- Summary
- T-motif1-motif2 right-left hybrid parallel g-quadruplex in complex with n-methylmesoporphyrin ix
- Reference
- Xing ER, Yatsunyk LA: "Preservation of left-handed fold and interaction with N-methylmesoporphyrin IX by two-block sequences with left-hand folding potential."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(+P+P+P), negative twist
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.152 type=planar O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 2 glyco-bond=---- sugar=---- groove=---- planarity=0.114 type=planar O+ nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG13 3 glyco-bond=---- sugar=---- groove=---- planarity=0.181 type=other O+ nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25 4 glyco-bond=---- sugar=---3 groove=---- planarity=0.117 type=planar O+ nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG27
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, 4 G-tetrads, INTRA-molecular, with 1 stem
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG4,A.DG7,A.DG10 3 glyco-bond=---- sugar=3--- groove=---- Major-->WC O+ nts=4 GGGG A.DG27,A.DG23,A.DG20,A.DG17 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG25,A.DG22,A.DG19,A.DG16 step#1 mp(<<,backward) area=6.14 rise=3.29 twist=35.7 step#2 mm(<>,outward) area=27.82 rise=3.33 twist=-8.9 step#3 pm(>>,forward) area=11.08 rise=3.23 twist=-27.2 strand#1 DNA glyco-bond=---- sugar=--3- nts=4 GGGG A.DG2,A.DG13,A.DG27,A.DG25 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG5,A.DG4,A.DG23,A.DG22 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG8,A.DG7,A.DG20,A.DG19 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG11,A.DG10,A.DG17,A.DG16 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG11 |
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2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG13,A.DG4,A.DG7,A.DG10 |
|
3 glyco-bond=---- sugar=3--- groove=---- Major-->WC O+ nts=4 GGGG A.DG27,A.DG23,A.DG20,A.DG17 |
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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, WARNING, 4+0, 2(+P+P+P), WARNING
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1 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG16,A.DG25,A.DG22,A.DG19 2 glyco-bond=---- sugar=-3-- groove=---- Major-->WC O+ nts=4 GGGG A.DG17,A.DG27,A.DG23,A.DG20 step#1 mp(<<,backward) area=11.08 rise=3.23 twist=-27.2 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG16,A.DG17 strand#2* U DNA glyco-bond=-- sugar=-3 nts=2 GG A.DG25,A.DG27 bulged-nts=1 T A.DT26 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG22,A.DG23 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG19,A.DG20 loop#1 type=propeller strands=[#1,#4] nts=1 T A.DT18 loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT21 loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT24 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG A.DG2,A.DT3,A.DG4,A.DG5 2* type=V-shaped helix=#1 nts=4 GGTG A.DG10,A.DG11,A.DT12,A.DG13