J3_5FDV_016

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

CGUCAG*CGCAACC*GACGACG

Length

20 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_016 not in the Motif Atlas

Homologous match to J3_4LFB_007

Geometric discrepancy: 0.0812

The information below is about J3_4LFB_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_08394.3

Basepair signature

cWW-tSS-F-F-tWH-F-F-cWW-F-cWW-F-F-F-F-F

Number of instances in this motif group

2

Unit IDs

5FDV|1|1a|C|1063
5FDV|1|1a|G|1064
5FDV|1|1a|U|1065
5FDV|1|1a|C|1066
5FDV|1|1a|A|1067
5FDV|1|1a|G|1068
*
5FDV|1|1a|C|1107
5FDV|1|1a|G|1108
5FDV|1|1a|C|1109
5FDV|1|1a|A|1110
5FDV|1|1a|A|1111
5FDV|1|1a|C|1112
5FDV|1|1a|C|1113
*
5FDV|1|1a|G|1187
5FDV|1|1a|A|1188
5FDV|1|1a|C|1189
5FDV|1|1a|G|1190
5FDV|1|1a|A|1191
5FDV|1|1a|C|1192
5FDV|1|1a|G|1193

Current chains

Chain 1a

16S ribosomal RNA

Nearby chains

Chain 1c

30S ribosomal protein S3

Chain 1e

30S ribosomal protein S5

Chain 1g

30S ribosomal protein S7

Chain 1i

30S ribosomal protein S9

Chain 1j

30S ribosomal protein S10

Chain 1n

30S ribosomal protein S14 type Z