DSSR-enabled G4 identification/annotation: PDB entry 4wo2
Summary information and primary citation
- PDB-id
- 4wo2
- Class
- DNA
- Method
- X-ray (1.82 Å)
- Summary
- Crystal structure of human native ckit proto-oncogene promoter quadruplex DNA
- Reference
- Wei D, Parkinson GN, Neidle S: "CRYSTAL STRUCTURE OF HUMAN NATIVE CKIT-1 PROTO-ONCOGENE PROMOTER QUADRUPLEX DNA."
- Abstract
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, UUUU, parallel, 4+0, 2(-PX+P), coaxial interfaces: 5'/5'-SEPARATED
Cartoon-block schematics in six views (download the tarball)
List of 6 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.201 type=other O+ nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13 2 glyco-bond=---- sugar=--3- groove=---- planarity=0.223 type=other N+ nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 3 glyco-bond=---- sugar=---- groove=---- planarity=0.367 type=bowl N+ nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15 4 glyco-bond=---- sugar=---- groove=---- planarity=0.206 type=other O+ nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13 5 glyco-bond=---- sugar=--3- groove=---- planarity=0.216 type=other N+ nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14 6 glyco-bond=---- sugar=---- groove=---- planarity=0.352 type=bowl N+ nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
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, 6 G-tetrads, inter-molecular, with 2 stems
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15 2 glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG13,B.DG10,B.DG6,B.DG2 5 glyco-bond=---- sugar=-3-- groove=---- Major-->WC N+ nts=4 GGGG B.DG14,B.DG21,B.DG7,B.DG3 6 glyco-bond=---- sugar=---- groove=---- Major-->WC N+ nts=4 GGGG B.DG15,B.DG22,B.DG8,B.DG4 step#1 mp(<<,backward) area=9.17 rise=3.39 twist=32.5 step#2 mp(<<,backward) area=11.04 rise=3.48 twist=29.2 step#3 mm(<>,outward) area=27.81 rise=3.38 twist=-8.2 step#4 pm(>>,forward) area=10.35 rise=3.44 twist=30.3 step#5 pm(>>,forward) area=9.34 rise=3.40 twist=32.2 strand#1 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG4,A.DG3,A.DG2,B.DG13,B.DG14,B.DG15 strand#2 DNA glyco-bond=------ sugar=----3- nts=6 GGGGGG A.DG8,A.DG7,A.DG6,B.DG10,B.DG21,B.DG22 strand#3 DNA glyco-bond=------ sugar=-3---- nts=6 GGGGGG A.DG22,A.DG21,A.DG10,B.DG6,B.DG7,B.DG8 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG15,A.DG14,A.DG13,B.DG2,B.DG3,B.DG4 |
| 5 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15 |
|
2 glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13 |
|
4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG B.DG13,B.DG10,B.DG6,B.DG2 |
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5 glyco-bond=---- sugar=-3-- groove=---- Major-->WC N+ nts=4 GGGG B.DG14,B.DG21,B.DG7,B.DG3 |
List of 2 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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-PX+P)
|
1 glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14 2 glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15 step#1 pm(>>,forward) area=9.17 rise=3.39 twist=32.5 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG3,A.DG4 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8 strand#3 U DNA glyco-bond=-- sugar=3- nts=2 GG A.DG21,A.DG22 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG14,A.DG15 loop#1 type=propeller strands=[#1,#2] nts=2 AG A.DA5,A.DG6 loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG A.DC9,A.DG10,A.DC11,A.DT12,A.DG13 loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG A.DA16,A.DG17,A.DG18,A.DA19,A.DG20 |
Stem#2, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-PX+P)
|
1 glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14 2 glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15 step#1 pm(>>,forward) area=9.34 rise=3.40 twist=32.2 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG3,B.DG4 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG7,B.DG8 strand#3 U DNA glyco-bond=-- sugar=3- nts=2 GG B.DG21,B.DG22 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG14,B.DG15 loop#1 type=propeller strands=[#1,#2] nts=2 AG B.DA5,B.DG6 loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG B.DC9,B.DG10,B.DC11,B.DT12,B.DG13 loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG B.DA16,B.DG17,B.DG18,B.DA19,B.DG20 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5'-SEPARATED]
List of 4 non-stem G4-loops (including the two closing Gs)
1* type=V-shaped helix=#1 nts=5 GGGCG A.DG6,A.DG7,A.DG8,A.DC9,A.DG10 2 type=lateral helix=#1 nts=4 GCTG A.DG10,A.DC11,A.DT12,A.DG13 3* type=V-shaped helix=#1 nts=5 GGGCG B.DG6,B.DG7,B.DG8,B.DC9,B.DG10 4 type=lateral helix=#1 nts=4 GCTG B.DG10,B.DC11,B.DT12,B.DG13