DSSR-enabled G4 identification/annotation: PDB entry 9mmf
Summary information and primary citation
- PDB-id
- 9mmf
- Class
- DNA
- Method
- X-ray (2.08 Å)
- Summary
- First structure of five-tetrad g-quadruplex
- Reference
- Eyiolowope J, Xing ER, Yatsunyk LA: "The first crystal structure of five-tetrad G-quadruplex."
- Abstract
- G4 notes
- 10 G-tetrads, 2 G4 helices, 2 G4 stems, UDUU, hybrid3, 3+1, 4(-Lw-Ln-P)
Cartoon-block schematics in six views (download the tarball)
List of 10 G-tetrads
1 glyco-bond=s-ss sugar=---- groove=wn-- planarity=0.182 type=other -- nts=4 GGGG 1:A.DG2,1:A.DG14,1:A.DG18,2:A.DG26 2 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.131 type=planar O+ nts=4 GGGG 1:A.DG3,1:A.DG13,1:A.DG19,1:A.DG27 3 glyco-bond=-s-- sugar=--3- groove=wn-- planarity=0.255 type=other O+ nts=4 GGGG 1:A.DG4,1:A.DG12,1:A.DG20,1:A.DG28 4 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.232 type=other O+ nts=4 GGGG 1:A.DG5,1:A.DG11,1:A.DG21,1:A.DG29 5 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.266 type=bowl O+ nts=4 GGGG 1:A.DG6,1:A.DG10,1:A.DG22,1:A.DG30 6 glyco-bond=ss-s sugar=---- groove=-wn- planarity=0.182 type=other -- nts=4 GGGG 1:A.DG26,2:A.DG2,2:A.DG14,2:A.DG18 7 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.131 type=planar O+ nts=4 GGGG 2:A.DG3,2:A.DG13,2:A.DG19,2:A.DG27 8 glyco-bond=-s-- sugar=--3- groove=wn-- planarity=0.255 type=other O+ nts=4 GGGG 2:A.DG4,2:A.DG12,2:A.DG20,2:A.DG28 9 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.232 type=other O+ nts=4 GGGG 2:A.DG5,2:A.DG11,2:A.DG21,2:A.DG29 10 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.266 type=bowl O+ nts=4 GGGG 2:A.DG6,2:A.DG10,2:A.DG22,2:A.DG30
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, 5 G-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC -- nts=4 GGGG 1:A.DG2,1:A.DG14,1:A.DG18,2:A.DG26 2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG13,1:A.DG19,1:A.DG27 3 glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG12,1:A.DG20,1:A.DG28 4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG5,1:A.DG11,1:A.DG21,1:A.DG29 5 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG6,1:A.DG10,1:A.DG22,1:A.DG30 step#1 mm(<>,outward) area=11.85 rise=3.45 twist=19.2 step#2 pm(>>,forward) area=9.03 rise=3.31 twist=31.8 step#3 pm(>>,forward) area=13.12 rise=3.48 twist=27.2 step#4 pm(>>,forward) area=14.99 rise=3.40 twist=25.2 strand#1 DNA glyco-bond=s---- sugar=----- nts=5 GGGGG 1:A.DG2,1:A.DG3,1:A.DG4,1:A.DG5,1:A.DG6 strand#2 DNA glyco-bond=-ssss sugar=----- nts=5 GGGGG 1:A.DG14,1:A.DG13,1:A.DG12,1:A.DG11,1:A.DG10 strand#3 DNA glyco-bond=s---- sugar=--3-- nts=5 GGGGG 1:A.DG18,1:A.DG19,1:A.DG20,1:A.DG21,1:A.DG22 strand#4 DNA glyco-bond=s---- sugar=----- nts=5 GGGGG 2:A.DG26,1:A.DG27,1:A.DG28,1:A.DG29,1:A.DG30 |
| 4 stacking diagrams | |
|
1 glyco-bond=s-ss sugar=---- groove=wn-- Major-->WC -- nts=4 GGGG 1:A.DG2,1:A.DG14,1:A.DG18,2:A.DG26 |
|
2 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG13,1:A.DG19,1:A.DG27 |
|
3 glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG12,1:A.DG20,1:A.DG28 |
|
4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG5,1:A.DG11,1:A.DG21,1:A.DG29 |
Helix#2, 5 G-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC -- nts=4 GGGG 1:A.DG26,2:A.DG2,2:A.DG14,2:A.DG18 2 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 2:A.DG27,2:A.DG3,2:A.DG13,2:A.DG19 3 glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major O+ nts=4 GGGG 2:A.DG28,2:A.DG4,2:A.DG12,2:A.DG20 4 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 2:A.DG29,2:A.DG5,2:A.DG11,2:A.DG21 5 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 2:A.DG30,2:A.DG6,2:A.DG10,2:A.DG22 step#1 mm(<>,outward) area=11.85 rise=3.45 twist=19.2 step#2 pm(>>,forward) area=9.03 rise=3.31 twist=31.8 step#3 pm(>>,forward) area=13.12 rise=3.48 twist=27.2 step#4 pm(>>,forward) area=14.98 rise=3.40 twist=25.2 strand#1 DNA glyco-bond=s---- sugar=----- nts=5 GGGGG 1:A.DG26,2:A.DG27,2:A.DG28,2:A.DG29,2:A.DG30 strand#2 DNA glyco-bond=s---- sugar=----- nts=5 GGGGG 2:A.DG2,2:A.DG3,2:A.DG4,2:A.DG5,2:A.DG6 strand#3 DNA glyco-bond=-ssss sugar=----- nts=5 GGGGG 2:A.DG14,2:A.DG13,2:A.DG12,2:A.DG11,2:A.DG10 strand#4 DNA glyco-bond=s---- sugar=--3-- nts=5 GGGGG 2:A.DG18,2:A.DG19,2:A.DG20,2:A.DG21,2:A.DG22 |
| 4 stacking diagrams | |
|
1 glyco-bond=ss-s sugar=---- groove=-wn- Major-->WC -- nts=4 GGGG 1:A.DG26,2:A.DG2,2:A.DG14,2:A.DG18 |
|
2 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 2:A.DG27,2:A.DG3,2:A.DG13,2:A.DG19 |
|
3 glyco-bond=--s- sugar=---3 groove=-wn- WC-->Major O+ nts=4 GGGG 2:A.DG28,2:A.DG4,2:A.DG12,2:A.DG20 |
|
4 glyco-bond=--s- sugar=---- groove=-wn- WC-->Major O+ nts=4 GGGG 2:A.DG29,2:A.DG5,2:A.DG11,2:A.DG21 |
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, 4 G-tetrads, 3 loops, INTRA-molecular, UDUU, hybrid3, 3+1, 4(-Lw-Ln-P)
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1 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG13,1:A.DG19,1:A.DG27 2 glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG12,1:A.DG20,1:A.DG28 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG5,1:A.DG11,1:A.DG21,1:A.DG29 4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 1:A.DG6,1:A.DG10,1:A.DG22,1:A.DG30 step#1 pm(>>,forward) area=9.03 rise=3.31 twist=31.8 step#2 pm(>>,forward) area=13.12 rise=3.48 twist=27.2 step#3 pm(>>,forward) area=14.99 rise=3.40 twist=25.2 strand#1 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG3,1:A.DG4,1:A.DG5,1:A.DG6 strand#2 D DNA glyco-bond=ssss sugar=---- nts=4 GGGG 1:A.DG13,1:A.DG12,1:A.DG11,1:A.DG10 strand#3 U DNA glyco-bond=---- sugar=-3-- nts=4 GGGG 1:A.DG19,1:A.DG20,1:A.DG21,1:A.DG22 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG27,1:A.DG28,1:A.DG29,1:A.DG30 loop#1 type=lateral strands=[#1,#2] nts=3 TTT 1:A.DT7,1:A.DT8,1:A.DT9 loop#2 type=lateral strands=[#2,#3] nts=5 GTTTG 1:A.DG14,1:A.DT15,1:A.DT16,1:A.DT17,1:A.DG18 loop#3 type=propeller strands=[#3,#4] nts=4 TTTG 1:A.DT23,1:A.DT24,1:A.DT25,1:A.DG26 |
Stem#2, 4 G-tetrads, 3 loops, INTRA-molecular, UDUU, hybrid3, 3+1, 4(-Lw-Ln-P)
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1 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 2:A.DG3,2:A.DG13,2:A.DG19,2:A.DG27 2 glyco-bond=-s-- sugar=--3- groove=wn-- WC-->Major O+ nts=4 GGGG 2:A.DG4,2:A.DG12,2:A.DG20,2:A.DG28 3 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 2:A.DG5,2:A.DG11,2:A.DG21,2:A.DG29 4 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG 2:A.DG6,2:A.DG10,2:A.DG22,2:A.DG30 step#1 pm(>>,forward) area=9.03 rise=3.31 twist=31.8 step#2 pm(>>,forward) area=13.12 rise=3.48 twist=27.2 step#3 pm(>>,forward) area=14.98 rise=3.40 twist=25.2 strand#1 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 2:A.DG3,2:A.DG4,2:A.DG5,2:A.DG6 strand#2 D DNA glyco-bond=ssss sugar=---- nts=4 GGGG 2:A.DG13,2:A.DG12,2:A.DG11,2:A.DG10 strand#3 U DNA glyco-bond=---- sugar=-3-- nts=4 GGGG 2:A.DG19,2:A.DG20,2:A.DG21,2:A.DG22 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 2:A.DG27,2:A.DG28,2:A.DG29,2:A.DG30 loop#1 type=lateral strands=[#1,#2] nts=3 TTT 2:A.DT7,2:A.DT8,2:A.DT9 loop#2 type=lateral strands=[#2,#3] nts=5 GTTTG 2:A.DG14,2:A.DT15,2:A.DT16,2:A.DT17,2:A.DG18 loop#3 type=propeller strands=[#3,#4] nts=4 TTTG 2:A.DT23,2:A.DT24,2:A.DT25,2:A.DG26 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=lateral helix=#1 nts=5 GTTTG 1:A.DG14,1:A.DT15,1:A.DT16,1:A.DT17,1:A.DG18 2 type=lateral helix=#2 nts=5 GTTTG 2:A.DG14,2:A.DT15,2:A.DT16,2:A.DT17,2:A.DG18