IL_5NDH_002

3D structure

PDB id

5NDH (explore in PDB, NAKB, or RNA 3D Hub)

Description

The structure of the G. violaceus guanidine II riboswitch P2 stem-loop

Experimental method

X-RAY DIFFRACTION

Resolution

1.81 Å

Loop

Sequence

G(CBV)G*CGC

Length

6 nucleotides

Bulged bases

None detected

QA status

Self-complementary:

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

IL_5NDH_002 not in the Motif Atlas

Geometric match to IL_3SZX_003

Geometric discrepancy: 0.1136

The information below is about IL_3SZX_003

Detailed Annotation

Isolated non-canonical cWW pair

Broad Annotation

Isolated non-canonical cWW pair

Motif group

IL_87907.2

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

179

Unit IDs

5NDH|1|B|G|1
5NDH|1|B|CBV|2
5NDH|1|B|G|3
*
5NDH|1|B|C|14
5NDH|1|B|G|15
5NDH|1|B|C|16

Current chains

Chain B

RNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')

Nearby chains

Chain C

RNA (5'-R(*GP*(CBV)P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3')