J3_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

CAAUG*CCCAGUUC*GCCG

Length

17 nucleotides

Bulged bases

5FDV|1|1a|U|1240

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_018 not in the Motif Atlas

Homologous match to J3_4LFB_009

Geometric discrepancy: 0.0977

The information below is about J3_4LFB_009

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_37047.6

Basepair signature

cWW-cSS-tHW-F-F-F-cWW-cWW-F-cSH-F-F

Number of instances in this motif group

4

Unit IDs

5FDV|1|1a|C|1237
5FDV|1|1a|A|1238
5FDV|1|1a|A|1239
5FDV|1|1a|U|1240
5FDV|1|1a|G|1241
*
5FDV|1|1a|C|1296
5FDV|1|1a|C|1297
5FDV|1|1a|C|1298
5FDV|1|1a|A|1299
5FDV|1|1a|G|1300
5FDV|1|1a|U|1301
5FDV|1|1a|U|1302
5FDV|1|1a|C|1303
*
5FDV|1|1a|G|1334
5FDV|1|1a|C|1335
5FDV|1|1a|C|1336
5FDV|1|1a|G|1337

Current chains

Chain 1a

16S ribosomal RNA

Nearby chains

Chain 1g

30S ribosomal protein S7

Chain 1m

30S ribosomal protein S13

Chain 1u

30S ribosomal protein Thx