J3_5FDV_073

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

CGC*GGACUGC*GAGGAAGGAG

Length

20 nucleotides

Bulged bases

5FDV|1|2a|A|1183

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_073 not in the Motif Atlas

Homologous match to J3_4LFB_018

Geometric discrepancy: 0.1203

The information below is about J3_4LFB_018

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17791.2

Basepair signature

cWW-F-cHW-cWW-tWH-cWW-F-tSW-tWS-cSH-cWW-cWW

Number of instances in this motif group

2

Unit IDs

5FDV|1|2a|C|1116
5FDV|1|2a|G|1117
5FDV|1|2a|C|1118
*
5FDV|1|2a|G|1155
5FDV|1|2a|G|1156
5FDV|1|2a|A|1157
5FDV|1|2a|C|1158
5FDV|1|2a|U|1159
5FDV|1|2a|G|1160
5FDV|1|2a|C|1161
*
5FDV|1|2a|G|1175
5FDV|1|2a|A|1176
5FDV|1|2a|G|1177
5FDV|1|2a|G|1178
5FDV|1|2a|A|1179
5FDV|1|2a|A|1180
5FDV|1|2a|G|1181
5FDV|1|2a|G|1182
5FDV|1|2a|A|1183
5FDV|1|2a|G|1184

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2b

30S ribosomal protein S2

Chain 2i

30S ribosomal protein S9

Chain 2n

30S ribosomal protein S14 type Z