IL_8K85_023

3D structure

PDB id

8K85 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of Red Broccoli aptamer with OBI

Experimental method

X-RAY DIFFRACTION

Resolution

2.95 Å

Loop

Sequence

AGUAGUGUGUGGGC*GACGGUCGGGU

Length

25 nucleotides

Bulged bases

8K85|1|A|A|43||||2_555, 8K85|1|A|U|47||||2_555, 8K85|1|B|U|9||||2_555

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

IL_8K85_023 not in the Motif Atlas

Geometric match to IL_4TS2_010

Geometric discrepancy: 0.1213

The information below is about IL_4TS2_010

Detailed Annotation

G-quadruplex

Broad Annotation

No text annotation

Motif group

IL_64858.3

Basepair signature

cWW-cHW-cWH-R-L-cWH-cHW-cHW-cWH-cWH-cHW-L-cWW-L-R-cWW-L-cWW

Number of instances in this motif group

6

Unit IDs

8K85|1|A|A|40||||2_555
8K85|1|A|G|41||||2_555
8K85|1|A|U|42||||2_555
8K85|1|A|A|43||||2_555
8K85|1|A|G|44||||2_555
8K85|1|A|U|45||||2_555
8K85|1|A|G|46||||2_555
8K85|1|A|U|47||||2_555
8K85|1|A|G|48||||2_555
8K85|1|A|U|49||||2_555
8K85|1|A|G|50||||2_555
8K85|1|A|G|51||||2_555
8K85|1|A|G|52||||2_555
8K85|1|A|C|53||||2_555
*
8K85|1|B|G|4||||2_555
8K85|1|B|A|5||||2_555
8K85|1|B|C|6||||2_555
8K85|1|B|G|7||||2_555
8K85|1|B|G|8||||2_555
8K85|1|B|U|9||||2_555
8K85|1|B|C|10||||2_555
8K85|1|B|G|11||||2_555
8K85|1|B|G|12||||2_555
8K85|1|B|G|13||||2_555
8K85|1|B|U|14||||2_555

Current chains

Chain A

RNA (56-MER)

Chain B

RNA (56-MER)

Nearby chains