IL_5NDW_075

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

GGAA*UC

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

IL_5NDW_075 not in the Motif Atlas

Homologous match to IL_5TBW_076

Geometric discrepancy: 0.0659

The information below is about IL_5TBW_076

Detailed Annotation

Major groove platform; stack outside cWW

Broad Annotation

Major groove platform

Motif group

IL_50694.4

Basepair signature

cWW-cWW-tSH-cWW-R

Number of instances in this motif group

28

Unit IDs

5NDW|1|1|G|1898
5NDW|1|1|G|1899
5NDW|1|1|A|1900
5NDW|1|1|A|1901
*
5NDW|1|1|U|2336
5NDW|1|1|C|2337

Current chains

Chain 1

25S ribosomal RNA

Nearby chains

Chain L3

60S ribosomal protein L3

Chain N3

60S ribosomal protein L23-A