J3_5FDU_040

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

CGAAG*CGCCAGAGAG*CGUAG

Length

20 nucleotides

Bulged bases

5FDU|1|1A|G|345

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_5FDU_040 not in the Motif Atlas

Homologous match to J3_9DFE_006

Geometric discrepancy: 0.0383

The information below is about J3_9DFE_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_46299.2

Basepair signature

cWW-F-F-F-cHH-cWW-tHS-F-cWW-cSW-tHS-cWW

Number of instances in this motif group

3

Unit IDs

5FDU|1|1A|C|321
5FDU|1|1A|G|322
5FDU|1|1A|A|323
5FDU|1|1A|A|324
5FDU|1|1A|G|325
*
5FDU|1|1A|C|340
5FDU|1|1A|G|341
5FDU|1|1A|C|342
5FDU|1|1A|C|343
5FDU|1|1A|A|344
5FDU|1|1A|G|345
5FDU|1|1A|A|346
5FDU|1|1A|G|347
5FDU|1|1A|A|348
5FDU|1|1A|G|349
*
5FDU|1|1A|C|361
5FDU|1|1A|G|362
5FDU|1|1A|U|363
5FDU|1|1A|A|364
5FDU|1|1A|G|365

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 1F

50S ribosomal protein L4

Chain 1Y

50S ribosomal protein L24