J3_5FDU_061

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

GGGACG*CC*GAAAAGC

Length

15 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_5FDU_061 not in the Motif Atlas

Homologous match to J3_9DFE_013

Geometric discrepancy: 0.0559

The information below is about J3_9DFE_013

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_34864.2

Basepair signature

cWW-F-cWW-F-tHH-F-tHS-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5FDU|1|2A|G|1424
5FDU|1|2A|G|1425
5FDU|1|2A|G|1426
5FDU|1|2A|A|1427
5FDU|1|2A|C|1428
5FDU|1|2A|G|1429
*
5FDU|1|2A|C|1564
5FDU|1|2A|C|1565
*
5FDU|1|2A|G|1568
5FDU|1|2A|A|1569
5FDU|1|2A|A|1570
5FDU|1|2A|A|1571
5FDU|1|2A|A|1572
5FDU|1|2A|G|1573
5FDU|1|2A|C|1574

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2