J5_5ND9_008

3D structure

PDB id

5ND9 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Hibernating ribosome from Staphylococcus aureus (Rotated state)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.7 Å

Loop

Sequence

CAAG*CGGACGGG*CAC*GAC*GGCAG

Length

23 nucleotides

Bulged bases

5ND9|1|a|A|108, 5ND9|1|a|C|360

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

J5_5ND9_008 not in the Motif Atlas

Homologous match to J5_4LFB_002

Geometric discrepancy: 0.1338

The information below is about J5_4LFB_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_58574.1

Basepair signature

cWW-F-tSS-cSS-F-cWW-cWW-cWW-F-F-cWW-F-F-cWW-cWW

Number of instances in this motif group

5

Unit IDs

5ND9|1|a|C|59
5ND9|1|a|A|60
5ND9|1|a|A|61
5ND9|1|a|G|62
*
5ND9|1|a|C|105
5ND9|1|a|G|106
5ND9|1|a|G|107
5ND9|1|a|A|108
5ND9|1|a|C|109
5ND9|1|a|G|110
5ND9|1|a|G|111
5ND9|1|a|G|112
*
5ND9|1|a|C|322
5ND9|1|a|A|323
5ND9|1|a|C|324
*
5ND9|1|a|G|345
5ND9|1|a|A|346
5ND9|1|a|C|347
*
5ND9|1|a|G|358
5ND9|1|a|G|359
5ND9|1|a|C|360
5ND9|1|a|A|361
5ND9|1|a|G|362

Current chains

Chain a

16S ribosomal RNA

Nearby chains

Chain N

50S ribosomal protein L14

Chain p

30S ribosomal protein S16

Chain t

30S ribosomal protein S20