HL_5J01_001

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

GUGAGAGUC

Length

9 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_5J01_001 not in the Motif Atlas

Geometric match to HL_3IGI_001

Geometric discrepancy: 0.1287

The information below is about HL_3IGI_001

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_33597.3

Basepair signature

cWW-tWH-F-F-F-F-F

Number of instances in this motif group

135

Unit IDs

5J01|1|A|G|30
5J01|1|A|U|31
5J01|1|A|G|32
5J01|1|A|A|33
5J01|1|A|G|34
5J01|1|A|A|35
5J01|1|A|G|36
5J01|1|A|U|37
5J01|1|A|C|38

Current chains

Chain A

group II intron lariat

Nearby chains