J3_5FDV_064

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|2A|G|2833, 5FDV|1|2A|A|2835

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_064 not in the Motif Atlas

Homologous match to J3_9DFE_019

Geometric discrepancy: 0.0983

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|2A|C|2814
5FDV|1|2A|C|2815
*
5FDV|1|2A|G|2831
5FDV|1|2A|U|2832
5FDV|1|2A|G|2833
5FDV|1|2A|G|2834
5FDV|1|2A|A|2835
5FDV|1|2A|U|2836
*
5FDV|1|2A|A|2882
5FDV|1|2A|A|2883
5FDV|1|2A|U|2884
5FDV|1|2A|C|2885
5FDV|1|2A|G|2886

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 25

50S ribosomal protein L32

Chain 2E

50S ribosomal protein L3

Chain 2R

50S ribosomal protein L17