J5_5NDV_009

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

AUAGUUCCUUUACUACAUGG*CAUGCUUAAAA*UG*CGA*UGGUU

Length

41 nucleotides

Bulged bases

5NDV|1|2|U|128, 5NDV|1|2|U|132, 5NDV|1|2|U|134, 5NDV|1|2|A|135, 5NDV|1|2|C|136, 5NDV|1|2|U|137, 5NDV|1|2|A|140, 5NDV|1|2|U|141, 5NDV|1|2|U|178

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

5NDV|1|2|A|124
5NDV|1|2|U|125
5NDV|1|2|A|126
5NDV|1|2|G|127
5NDV|1|2|U|128
5NDV|1|2|U|129
5NDV|1|2|C|130
5NDV|1|2|C|131
5NDV|1|2|U|132
5NDV|1|2|U|133
5NDV|1|2|U|134
5NDV|1|2|A|135
5NDV|1|2|C|136
5NDV|1|2|U|137
5NDV|1|2|A|138
5NDV|1|2|C|139
5NDV|1|2|A|140
5NDV|1|2|U|141
5NDV|1|2|G|142
5NDV|1|2|G|143
*
5NDV|1|2|C|172
5NDV|1|2|A|173
5NDV|1|2|U|174
5NDV|1|2|G|175
5NDV|1|2|C|176
5NDV|1|2|U|177
5NDV|1|2|U|178
5NDV|1|2|A|179
5NDV|1|2|A|180
5NDV|1|2|A|181
5NDV|1|2|A|182
*
5NDV|1|2|U|203
5NDV|1|2|G|204
*
5NDV|1|2|C|263
5NDV|1|2|G|264
5NDV|1|2|A|265
*
5NDV|1|2|U|289
5NDV|1|2|G|290
5NDV|1|2|G|291
5NDV|1|2|U|292
5NDV|1|2|U|293

Current chains

Chain 2

18S ribosomal RNA

Nearby chains

Chain S4

40S ribosomal protein S4-A

Chain S6

40S ribosomal protein S6-A

Chain S8

40S ribosomal protein S8-A