Annotating tertiary motifs in RNA structures

2GDI - TPP riboswitch

Statistics of tertiary motifs

Motif	Number
Coaxial helix	6
A-minor	4
Ribose zipper	2
Pseudoknot	0
Loop-loop receptor	2
D-loop;T-loop	0
Kissing hairpin	1

Annotated diagram (PDF, EPS)

Structure information of tertiary motifs

Coaxial helix

ID	Strand 1		Strand 2
ID	Seq num	Chain	Seq num	Chain
1	10-19	X	47-51,85-89	X
2	21-23,25-27	X	33-38	X
3	56-61,63-66	X	73-78,80-83	X
4	10-19	Y	47-51,85-89	Y
5	21-23,25-27	Y	33-38	Y
6	56-61,63-66	Y	73-78,80-83	Y

A-minor

ID	Residue 1			Residue 2			Residue 3
ID	Seq	Seq num	Chain	Seq	Seq num	Chain	Seq	Seq num	Chain
1	A	56	X	G	17	X	C	49	X
2	A	56	Y	G	17	Y	C	49	Y
3	A	84	X	C	50	X	G	16	X
4	A	84	Y	C	50	Y	G	16	Y

Ribose zipper

ID	Strand 1			Strand 2
ID	Seq	Seq num	Chain	Seq	Seq num	Chain
1	5′-GC-3′	21,22	Y	5′-AU-3′	70,71	Y
2	5′-GC-3′	21,22	X	5′-AU-3′	70,71	X

Loop-loop receptor

ID	Loop		Receptor
ID	Seq num	Chain	Seq num	Chain
1	68-71	X	37-38,21-24	X
2	68-71	Y	37-38,21-24	Y

Kissing hairpin

ID	Strand 1		Strand 2
ID	Seq num	Chain	Seq num	Chain
1	29-30	X	29-30	Y