J4_5NDG_012

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

AAG*CGAAAG*CCAUAAACUAUG*UU

Length

23 nucleotides

Bulged bases

5NDG|1|2|A|623, 5NDG|1|2|A|1026, 5NDG|1|2|U|1029, 5NDG|1|2|U|1031

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

J4_5NDG_012 not in the Motif Atlas

Homologous match to J4_8P9A_022

Geometric discrepancy: 0.0715

The information below is about J4_8P9A_022

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61885.6

Basepair signature

cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F

Number of instances in this motif group

4

Unit IDs

5NDG|1|2|A|622
5NDG|1|2|A|623
5NDG|1|2|G|624
*
5NDG|1|2|C|975
5NDG|1|2|G|976
5NDG|1|2|A|977
5NDG|1|2|A|978
5NDG|1|2|A|979
5NDG|1|2|G|980
*
5NDG|1|2|C|1021
5NDG|1|2|C|1022
5NDG|1|2|A|1023
5NDG|1|2|U|1024
5NDG|1|2|A|1025
5NDG|1|2|A|1026
5NDG|1|2|A|1027
5NDG|1|2|C|1028
5NDG|1|2|U|1029
5NDG|1|2|A|1030
5NDG|1|2|U|1031
5NDG|1|2|G|1032
*
5NDG|1|2|U|1103
5NDG|1|2|U|1104

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain 1

Large subunit ribosomal RNA; LSU rRNA

Chain C1

40S ribosomal protein S11-A

Chain C3

40S ribosomal protein S13

Chain C4

40S ribosomal protein S14-A

Chain D2

40S ribosomal protein S22-A

Chain D3

40S ribosomal protein S23-A

Chain D6

40S ribosomal protein S26-B

Chain Q1

60S ribosomal protein L41-A