J4_5FDU_003

3D structure

PDB id

5FDU (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Metalnikowin I antimicrobial peptide bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.9 Å

Loop

Sequence

CGAUAAA*UC*GCGC*GG

Length

15 nucleotides

Bulged bases

5FDU|1|1A|G|1317, 5FDU|1|1A|A|1318, 5FDU|1|1A|U|1319, 5FDU|1|1A|G|1694

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_5FDU_003 not in the Motif Atlas

Homologous match to J4_9DFE_003

Geometric discrepancy: 0.0411

The information below is about J4_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_64571.5

Basepair signature

cWW-F-cWW-tSS-cWW-F-cWW

Number of instances in this motif group

4

Unit IDs

5FDU|1|1A|C|1316
5FDU|1|1A|G|1317
5FDU|1|1A|A|1318
5FDU|1|1A|U|1319
5FDU|1|1A|A|1320
5FDU|1|1A|A|1321
5FDU|1|1A|A|1322
*
5FDU|1|1A|U|1340
5FDU|1|1A|C|1341
*
5FDU|1|1A|G|1692
5FDU|1|1A|C|1693
5FDU|1|1A|G|1694
5FDU|1|1A|C|1695
*
5FDU|1|1A|G|2031
5FDU|1|1A|G|2032

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 15

50S ribosomal protein L32

Chain 1R

50S ribosomal protein L17

Chain 1W

50S ribosomal protein L22