J4_5FDV_004

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

GGUUC*GGUUAG*CU*ACCCGUAC

Length

21 nucleotides

Bulged bases

5FDV|1|1A|U|1387

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_004 not in the Motif Atlas

Homologous match to J4_9DFE_004

Geometric discrepancy: 0.0456

The information below is about J4_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_69051.6

Basepair signature

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

Number of instances in this motif group

7

Unit IDs

5FDV|1|1A|G|1356
5FDV|1|1A|G|1357
5FDV|1|1A|U|1358
5FDV|1|1A|U|1359
5FDV|1|1A|C|1360
*
5FDV|1|1A|G|1384
5FDV|1|1A|G|1385
5FDV|1|1A|U|1386
5FDV|1|1A|U|1387
5FDV|1|1A|A|1388
5FDV|1|1A|G|1389
*
5FDV|1|1A|C|1450
5FDV|1|1A|U|1451
*
5FDV|1|1A|A|1643
5FDV|1|1A|C|1644
5FDV|1|1A|C|1645
5FDV|1|1A|C|1646
5FDV|1|1A|G|1647
5FDV|1|1A|U|1648
5FDV|1|1A|A|1649
5FDV|1|1A|C|1650

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 17

50S ribosomal protein L34

Chain 1X

50S ribosomal protein L23