J5_5FDV_018

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

CUGG*CUUG*CUGAAC*GGUAAUAG*CGAG

Length

26 nucleotides

Bulged bases

None detected

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

J5_5FDV_018 not in the Motif Atlas

Homologous match to J5_4LFB_001

Geometric discrepancy: 0.0703

The information below is about J5_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_70703.1

Basepair signature

cWW-F-tWH-F-F-cWW-cWW-cWH-cWH-cWW-tSH-tWH-tHW-tHS-cWW

Number of instances in this motif group

1

Unit IDs

5FDV|1|2a|C|36
5FDV|1|2a|U|37
5FDV|1|2a|G|38
5FDV|1|2a|G|39
*
5FDV|1|2a|C|403
5FDV|1|2a|U|404
5FDV|1|2a|U|405
5FDV|1|2a|G|406
*
5FDV|1|2a|C|436
5FDV|1|2a|U|437
5FDV|1|2a|G|438
5FDV|1|2a|A|439
5FDV|1|2a|A|441
5FDV|1|2a|C|442
*
5FDV|1|2a|G|492
5FDV|1|2a|G|493
5FDV|1|2a|U|494
5FDV|1|2a|A|495
5FDV|1|2a|A|496
5FDV|1|2a|U|498
5FDV|1|2a|A|499
5FDV|1|2a|G|500
*
5FDV|1|2a|C|545
5FDV|1|2a|G|546
5FDV|1|2a|A|547
5FDV|1|2a|G|548

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2d

30S ribosomal protein S4

Chain 2l

30S ribosomal protein S12