IL_5ND8_065

3D structure

PDB id

5ND8 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Hibernating ribosome from Staphylococcus aureus (Unrotated state)

Experimental method

ELECTRON MICROSCOPY

Resolution

3.7 Å

Loop

Sequence

CCGG*CG

Length

6 nucleotides

Bulged bases

5ND8|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_5ND8_065 not in the Motif Atlas

Homologous match to IL_7RQB_071

Geometric discrepancy: 0.1628

The information below is about IL_7RQB_071

Detailed Annotation

Minor groove platform, major groove intercalation

Broad Annotation

Minor groove platform, major groove intercalation

Motif group

IL_88739.3

Basepair signature

cWW-L-cWW

Number of instances in this motif group

11

Unit IDs

5ND8|1|A|C|1864
5ND8|1|A|C|1865
5ND8|1|A|G|1866
5ND8|1|A|G|1867
*
5ND8|1|A|C|1929
5ND8|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