J3_5FDV_054

3D structure

PDB id

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

Description

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

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

UG*UGUUG*CGCAA

Length

12 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_5FDV_054 not in the Motif Atlas

Homologous match to J3_6CZR_024

Geometric discrepancy: 0.1403

The information below is about J3_6CZR_024

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_04260.1

Basepair signature

cWW-F-F-F-F-F-cWW-cWW

Number of instances in this motif group

2

Unit IDs

5FDV|1|1a|U|1073
5FDV|1|1a|G|1074
*
5FDV|1|1a|U|1083
5FDV|1|1a|G|1084
5FDV|1|1a|U|1085
5FDV|1|1a|U|1086
5FDV|1|1a|G|1087
*
5FDV|1|1a|C|1098
5FDV|1|1a|G|1099
5FDV|1|1a|C|1100
5FDV|1|1a|A|1101
5FDV|1|1a|A|1102

Current chains

Chain 1a

16S ribosomal RNA

Nearby chains

Chain 1b

30S ribosomal protein S2

Chain 1e

30S ribosomal protein S5