IL_5NDW_451

3D structure

PDB id

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

Description

Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

3.7 Å

Loop

Sequence

GAAAGCA*UUAAGC

Length

13 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

IL_5NDW_451 not in the Motif Atlas

Homologous match to IL_5TBW_373

Geometric discrepancy: 0.0695

The information below is about IL_5TBW_373

Detailed Annotation

Minor groove platform related

Broad Annotation

No text annotation

Motif group

IL_10207.3

Basepair signature

cWW-cWW-L-cSW-L-R-L-cWW-R-cWW

Number of instances in this motif group

2

Unit IDs

5NDW|1|7|G|21
5NDW|1|7|A|22
5NDW|1|7|A|23
5NDW|1|7|A|24
5NDW|1|7|G|25
5NDW|1|7|C|26
5NDW|1|7|A|27
*
5NDW|1|7|U|53
5NDW|1|7|U|54
5NDW|1|7|A|55
5NDW|1|7|A|56
5NDW|1|7|G|57
5NDW|1|7|C|58

Current chains

Chain 7

5S ribosomal RNA

Nearby chains

Chain l5

60S ribosomal protein L5

Chain m1

60S ribosomal protein L11-B