HL_5J01_002

3D structure

PDB id

5J01 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Structure of the lariat form of a chimeric derivative of the Oceanobacillus iheyensis group II intron in the presence of NH4+ and MG2+.

Experimental method

X-RAY DIFFRACTION

Resolution

3.39 Å

Loop

Sequence

UGAAGGCAGAAGUAA

Length

15 nucleotides

Bulged bases

5J01|1|A|A|50

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_5J01_002 not in the Motif Atlas

Geometric match to HL_3IGI_002

Geometric discrepancy: 0.2154

The information below is about HL_3IGI_002

Detailed Annotation

Pseudoknot geometry with G-bulge

Broad Annotation

No text annotation

Motif group

HL_94488.1

Basepair signature

cWW-tSH-tHW-F-F-F-F-F-F

Number of instances in this motif group

2

Unit IDs

5J01|1|A|U|47
5J01|1|A|G|48
5J01|1|A|A|49
5J01|1|A|A|50
5J01|1|A|G|51
5J01|1|A|G|52
5J01|1|A|C|53
5J01|1|A|A|54
5J01|1|A|G|55
5J01|1|A|A|56
5J01|1|A|A|57
5J01|1|A|G|58
5J01|1|A|U|59
5J01|1|A|A|60
5J01|1|A|A|61

Current chains

Chain A

group II intron lariat

Nearby chains