IL_5VJB_004

3D structure

PDB id

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

Description

Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa

Experimental method

X-RAY DIFFRACTION

Resolution

2.1 Å

Loop

Sequence

CGG*C(5BU)G

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_5VJB_004 not in the Motif Atlas

Geometric match to IL_6IA2_005

Geometric discrepancy: 0.0874

The information below is about IL_6IA2_005

Detailed Annotation

Isolated non-canonical cWW pair

Broad Annotation

No text annotation

Motif group

IL_01003.5

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

238

Unit IDs

5VJB|1|D|C|2
5VJB|1|D|G|3
5VJB|1|D|G|4
*
5VJB|1|D|C|13
5VJB|1|D|5BU|14
5VJB|1|D|G|15

Current chains

Chain D

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

Nearby chains

Chain C

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