HL_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

GACGAC

Length

6 nucleotides

Bulged bases

None detected

QA status

Valid loop

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

HL_5VJB_004 not in the Motif Atlas

Geometric match to HL_5VJ9_003

Geometric discrepancy: 0.0638

The information below is about HL_5VJ9_003

Detailed Annotation

Pseudoknot geometry with 3' bulge

Broad Annotation

No text annotation

Motif group

HL_49081.1

Basepair signature

cWW-F-F-F

Number of instances in this motif group

17

Unit IDs

5VJB|1|D|G|6
5VJB|1|D|A|7
5VJB|1|D|C|8
5VJB|1|D|G|9
5VJB|1|D|A|10
5VJB|1|D|C|11

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 A

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

Chain B

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

Chain C

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