HL_5NDG_141

3D structure

PDB id

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

Description

Crystal structure of geneticin (G418) bound to the yeast 80S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

3.7 Å

Loop

Sequence

AGCAGUU

Length

7 nucleotides

Bulged bases

5NDG|1|5|G|1507, 5NDG|1|5|U|1511

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_5NDG_141 not in the Motif Atlas

Homologous match to HL_8C3A_032

Geometric discrepancy: 0.104

The information below is about HL_8C3A_032

Detailed Annotation

Pseudoknot geometry with 3' bulge

Broad Annotation

No text annotation

Motif group

HL_40756.1

Basepair signature

cWW-F-F-F

Number of instances in this motif group

14

Unit IDs

5NDG|1|5|A|1506
5NDG|1|5|G|1507
5NDG|1|5|C|1508
5NDG|1|5|A|1509
5NDG|1|5|G|1510
5NDG|1|5|U|1511
5NDG|1|5|U|1512

Current chains

Chain 5

25S ribosomal RNA

Nearby chains

Chain m7

60S ribosomal protein L17-A

Chain m9

60S ribosomal protein L19-A

Chain o9

60S ribosomal protein L39