HL_5NDV_202

3D structure

PDB id

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

Description

Crystal structure of Paromomycin bound to the yeast 80S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

3.3 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_5NDV_202 not in the Motif Atlas

Homologous match to HL_4V88_205

Geometric discrepancy: 0.3407

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

5NDV|1|6|A|829
5NDV|1|6|U|830
5NDV|1|6|U|831
5NDV|1|6|U|832
5NDV|1|6|U|833
5NDV|1|6|G|834
5NDV|1|6|U|835
5NDV|1|6|U|836
5NDV|1|6|G|837
5NDV|1|6|G|838
5NDV|1|6|U|839
5NDV|1|6|U|840
5NDV|1|6|U|841
5NDV|1|6|C|842
5NDV|1|6|U|843

Current chains

Chain 6

18S ribosomal RNA

Nearby chains

Chain c1

40S ribosomal protein S11-A