J3_5NDG_020

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

CCAG*CUAGUAA*UGAUUACG

Length

19 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

J3_5NDG_020 not in the Motif Atlas

Homologous match to J3_4V88_035

Geometric discrepancy: 0.1162

The information below is about J3_4V88_035

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_25303.1

Basepair signature

cWW-tSH-tHW-cSH-cSS-tHH-cSS-tWW-F-tHS-cWW-cWW

Number of instances in this motif group

5

Unit IDs

5NDG|1|2|C|1161
5NDG|1|2|C|1162
5NDG|1|2|A|1163
5NDG|1|2|G|1164
*
5NDG|1|2|C|1581
5NDG|1|2|U|1582
5NDG|1|2|A|1583
5NDG|1|2|G|1584
5NDG|1|2|U|1585
5NDG|1|2|A|1586
5NDG|1|2|A|1587
*
5NDG|1|2|U|1609
5NDG|1|2|G|1610
5NDG|1|2|A|1611
5NDG|1|2|U|1612
5NDG|1|2|U|1613
5NDG|1|2|A|1614
5NDG|1|2|C|1615
5NDG|1|2|G|1616

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C6

40S ribosomal protein S16-A

Chain D8

40S ribosomal protein S28-A

Chain S5

40S ribosomal protein S5