J3_5FDV_045

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

CC*GUGGAU*AAUCG

Length

13 nucleotides

Bulged bases

5FDV|1|1A|G|2843, 5FDV|1|1A|A|2845

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

J3_5FDV_045 not in the Motif Atlas

Homologous match to J3_9DFE_019

Geometric discrepancy: 0.0582

The information below is about J3_9DFE_019

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_76911.2

Basepair signature

cWW-tHS-F-F-F-cWW-cWW

Number of instances in this motif group

4

Unit IDs

5FDV|1|1A|C|2824
5FDV|1|1A|C|2825
*
5FDV|1|1A|G|2841
5FDV|1|1A|U|2842
5FDV|1|1A|G|2843
5FDV|1|1A|G|2844
5FDV|1|1A|A|2845
5FDV|1|1A|U|2846
*
5FDV|1|1A|A|2892
5FDV|1|1A|A|2893
5FDV|1|1A|U|2894
5FDV|1|1A|C|2895
5FDV|1|1A|G|2896

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 15

50S ribosomal protein L32

Chain 1E

50S ribosomal protein L3

Chain 1R

50S ribosomal protein L17