IL_5ND9_063

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

CCGG*CG

Length

6 nucleotides

Bulged bases

5ND9|1|A|C|1865

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

IL_5ND9_063 not in the Motif Atlas

Homologous match to IL_5J7L_314

Geometric discrepancy: 0.1565

The information below is about IL_5J7L_314

Detailed Annotation

Minor groove platform, major groove intercalation

Broad Annotation

Minor groove platform, major groove intercalation

Motif group

IL_95583.2

Basepair signature

cWW-L-cWW

Number of instances in this motif group

11

Unit IDs

5ND9|1|A|C|1864
5ND9|1|A|C|1865
5ND9|1|A|G|1866
5ND9|1|A|G|1867
*
5ND9|1|A|C|1929
5ND9|1|A|G|1930

Current chains

Chain A

23S ribosomal RNA

Nearby chains

Chain D

50S ribosomal protein L2

Chain a

Small subunit ribosomal RNA; SSU rRNA