J3_5FDV_028

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

CAAG*CUAGUAA*UGAAUACG

Length

19 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

J3_5FDV_028 not in the Motif Atlas

Homologous match to J3_4LFB_002

Geometric discrepancy: 0.0791

The information below is about J3_4LFB_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_25303.4

Basepair signature

cWW-F-F-cSS-F-cWW-tWW-F-tWH-F-tHS-cSH-cWW

Number of instances in this motif group

4

Unit IDs

5FDV|1|2a|C|936
5FDV|1|2a|A|937
5FDV|1|2a|A|938
5FDV|1|2a|G|939
*
5FDV|1|2a|C|1344
5FDV|1|2a|U|1345
5FDV|1|2a|A|1346
5FDV|1|2a|G|1347
5FDV|1|2a|U|1348
5FDV|1|2a|A|1349
5FDV|1|2a|A|1350
*
5FDV|1|2a|U|1372
5FDV|1|2a|G|1373
5FDV|1|2a|A|1374
5FDV|1|2a|A|1375
5FDV|1|2a|U|1376
5FDV|1|2a|A|1377
5FDV|1|2a|C|1378
5FDV|1|2a|G|1379

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2g

30S ribosomal protein S7

Chain 2i

30S ribosomal protein S9