J5_5NDG_019

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

ACUUUG*UUUCCU*ACUUU*AUAGAAUAGGA*UAAUGAU

Length

35 nucleotides

Bulged bases

5NDG|1|2|U|638, 5NDG|1|2|U|694, 5NDG|1|2|C|696, 5NDG|1|2|C|697, 5NDG|1|2|A|811, 5NDG|1|2|U|813, 5NDG|1|2|G|815, 5NDG|1|2|A|856

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

5NDG|1|2|A|636
5NDG|1|2|C|637
5NDG|1|2|U|638
5NDG|1|2|U|639
5NDG|1|2|U|640
5NDG|1|2|G|641
*
5NDG|1|2|U|693
5NDG|1|2|U|694
5NDG|1|2|U|695
5NDG|1|2|C|696
5NDG|1|2|C|697
5NDG|1|2|U|698
*
5NDG|1|2|A|740
5NDG|1|2|C|741
5NDG|1|2|U|742
5NDG|1|2|U|743
5NDG|1|2|U|744
*
5NDG|1|2|A|807
5NDG|1|2|U|808
5NDG|1|2|A|809
5NDG|1|2|G|810
5NDG|1|2|A|811
5NDG|1|2|A|812
5NDG|1|2|U|813
5NDG|1|2|A|814
5NDG|1|2|G|815
5NDG|1|2|G|816
5NDG|1|2|A|817
*
5NDG|1|2|U|854
5NDG|1|2|A|855
5NDG|1|2|A|856
5NDG|1|2|U|857
5NDG|1|2|G|858
5NDG|1|2|A|859
5NDG|1|2|U|860

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain C1

40S ribosomal protein S11-A

Chain C3

40S ribosomal protein S13

Chain D2

40S ribosomal protein S22-A

Chain M9

60S ribosomal protein L19-A

Chain S7

40S ribosomal protein S7-A