IL_5FDV_251

3D structure

PDB id

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

Description

Crystal structure of the Pyrrhocoricin antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

CGAAA(5MU)UC(5MC)UUG*C(5MC)UG

Length

16 nucleotides

Bulged bases

5FDV|1|2A|A|1938, 5FDV|1|2A|U|1944, 5FDV|1|2A|U|1963

QA status

Modified nucleotides: 5MU, 5MC

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_5FDV_251 not in the Motif Atlas

Homologous match to IL_7RQB_077

Geometric discrepancy: 0.0447

The information below is about IL_7RQB_077

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

5FDV|1|2A|C|1934
5FDV|1|2A|G|1935
5FDV|1|2A|A|1936
5FDV|1|2A|A|1937
5FDV|1|2A|A|1938
5FDV|1|2A|5MU|1939
5FDV|1|2A|U|1940
5FDV|1|2A|C|1941
5FDV|1|2A|5MC|1942
5FDV|1|2A|U|1943
5FDV|1|2A|U|1944
5FDV|1|2A|G|1945
*
5FDV|1|2A|C|1961
5FDV|1|2A|5MC|1962
5FDV|1|2A|U|1963
5FDV|1|2A|G|1964

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA