J4_5FDV_024

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

GAGUAACG*UC*GUAG*CC

Length

16 nucleotides

Bulged bases

5FDV|1|2a|C|121

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

J4_5FDV_024 not in the Motif Atlas

Homologous match to J4_4LFB_001

Geometric discrepancy: 0.065

The information below is about J4_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_35578.3

Basepair signature

cWW-F-cWW-F-F-F-tHW-F-cWW-cWW

Number of instances in this motif group

2

Unit IDs

5FDV|1|2a|G|115
5FDV|1|2a|A|116
5FDV|1|2a|G|117
5FDV|1|2a|U|118
5FDV|1|2a|A|119
5FDV|1|2a|A|120
5FDV|1|2a|C|121
5FDV|1|2a|G|122
*
5FDV|1|2a|U|239
5FDV|1|2a|C|240
*
5FDV|1|2a|G|286
5FDV|1|2a|U|287
5FDV|1|2a|A|288
5FDV|1|2a|G|289
*
5FDV|1|2a|C|311
5FDV|1|2a|C|312

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2p

30S ribosomal protein S16

Chain 2q

30S ribosomal protein S17