J4_5FDU_020

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

GACUG*CACAG*CGAC*GUAAC

Length

19 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

J4_5FDU_020 not in the Motif Atlas

Homologous match to J4_9DFE_007

Geometric discrepancy: 0.0436

The information below is about J4_9DFE_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61477.5

Basepair signature

cWW-tSW-F-tHS-tHS-F-cWW-cWW-F-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5FDU|1|2A|G|1772
5FDU|1|2A|A|1773
5FDU|1|2A|C|1774
5FDU|1|2A|U|1775
5FDU|1|2A|G|1776
*
5FDU|1|2A|C|1788
5FDU|1|2A|A|1789
5FDU|1|2A|C|1790
5FDU|1|2A|A|1791
5FDU|1|2A|G|1792
*
5FDU|1|2A|C|1827
5FDU|1|2A|G|1828
5FDU|1|2A|A|1829
5FDU|1|2A|C|1830
*
5FDU|1|2A|G|1975
5FDU|1|2A|U|1976
5FDU|1|2A|A|1977
5FDU|1|2A|A|1978
5FDU|1|2A|C|1979

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA