J3_5FDV_003

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

GGA*UUUAAAG*CAC

Length

13 nucleotides

Bulged bases

None detected

QA status

Unknown status

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_003 not in the Motif Atlas

Homologous match to J3_6PRV_001

Geometric discrepancy: 0.1557

The information below is about J3_6PRV_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_28621.5

Basepair signature

cWW-tSS-cSS-tSH-cWW-cWW-tWW-F-F

Number of instances in this motif group

7

Unit IDs

5FDV|1|1A|G|1101
5FDV|1|1A|G|1102
5FDV|1|1A|A|1103
*
5FDV|1|1A|U|1127
5FDV|1|1A|U|1128
5FDV|1|1A|U|1129
5FDV|1|1A|A|1130
5FDV|1|1A|A|1131
5FDV|1|1A|A|1132
5FDV|1|1A|G|1133
*
5FDV|1|1A|C|1148
5FDV|1|1A|A|1149
5FDV|1|1A|C|1150

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L36