Motif | SCOR class | tmRNA Res. | Source Res. | Coordinates | Comments |
---|---|---|---|---|---|
1 |  | 1–7, 353–363 | 1–7, 12–22 | 1IKD.pdb (chain W) | ACCA end and G3-U357 pair |
2 |  | 8–28, 325–352 | 8–28, 325–352 | tmx-34.pdb from tmRDB |  |
3a | internal loop with unpaired stacked bases | 29–33, 321–324 | 1775–1779, 1765–1768 | 1JJ2.pdb |  |
3b | stacked duplex with one non-WC pair | C35, A319 | Â | ERNA-3D | Â |
4 | stacked duplex with two non-WC pairs | 38–39, 315–316 | 2874–2875, 2882–2883 | 1JJ2.pdb |  |
5 |  | 309–311 |  | ERNA-3D |  |
6a | pseudoknot | 49–78 | 1–33 | 1RNK.pdb | pk1 |
6b | tetraloop | 87–98 | 5–8 | 1AFX.pdb | the only YRRR tetraloop in SCOR |
7 | nonaloop | 118–126 | 1834–1842 | 1JJ2.pdb |  |
8 | one unpaired and stacked U | U131 | U30 | 1B36.pdb | Â |
9 |  | 171–174 |  | ERNA-3D |  |
10a | stacked duplex with two non-WC pairs | 149–150, 165–166 | 288–289, 363–364 | 1JJ2.pdb |  |
10b | pseudoknot | 138–196 |  | 6a | pk2 |
11a | internal loop | 204–206, 223–225 | 780–782, 800–802 | 1J5E.pdb |  |
11b | pseudoknot | 197–247 |  | 6a | pk3 |
12 | stacked duplex with one non-WC pair | G258, A273 | A-G6, B-A27 | 420D.pdb | Â |
13a | stacked duplex with one non-WC pair | C266, U296 | Â | ERNA-3D | Â |
13b | pseudoknot | 248–299 |  | 6a | pk4 |