HL_5NDW_090

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

AUUUUGUUGGUUUCU

Length

15 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_5NDW_090 not in the Motif Atlas

Homologous match to HL_4V88_205

Geometric discrepancy: 0.2574

The information below is about HL_4V88_205

Detailed Annotation

Pseudoknot geometry

Broad Annotation

No text annotation

Motif group

HL_88364.1

Basepair signature

cWW-cWW-F-F-F-F-F-F-F-F-F-F-F

Number of instances in this motif group

3

Unit IDs

5NDW|1|2|A|829
5NDW|1|2|U|830
5NDW|1|2|U|831
5NDW|1|2|U|832
5NDW|1|2|U|833
5NDW|1|2|G|834
5NDW|1|2|U|835
5NDW|1|2|U|836
5NDW|1|2|G|837
5NDW|1|2|G|838
5NDW|1|2|U|839
5NDW|1|2|U|840
5NDW|1|2|U|841
5NDW|1|2|C|842
5NDW|1|2|U|843

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C1

40S ribosomal protein S11-A