J4_5FDU_025

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

GAG*CAUGUG*CAAAG*CGC

Length

17 nucleotides

Bulged bases

5FDU|1|2a|A|197

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_025 not in the Motif Atlas

Homologous match to J4_4LFB_002

Geometric discrepancy: 0.0928

The information below is about J4_4LFB_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_88771.1

Basepair signature

cWW-tSS-cWW-tSS-cWW-cWW-tWH-tWH-cSH-cWW

Number of instances in this motif group

1

Unit IDs

5FDU|1|2a|G|142
5FDU|1|2a|A|143
5FDU|1|2a|G|144
*
5FDU|1|2a|C|178
5FDU|1|2a|A|179
5FDU|1|2a|U|180
5FDU|1|2a|G|181
5FDU|1|2a|U|182
5FDU|1|2a|G|183
*
5FDU|1|2a|C|194
5FDU|1|2a|A|195
5FDU|1|2a|A|196
5FDU|1|2a|A|197
5FDU|1|2a|G|198
*
5FDU|1|2a|C|219
5FDU|1|2a|G|220
5FDU|1|2a|C|221

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2t

30S ribosomal protein S20