J3_5HCQ_032

3D structure

PDB id

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

Description

Crystal structure of antimicrobial peptide Oncocin d15-19 bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

CAAUG*CCCAGUUC*GCCG

Length

17 nucleotides

Bulged bases

5HCQ|1|2a|U|1222

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_5HCQ_032 not in the Motif Atlas

Homologous match to J3_4LFB_009

Geometric discrepancy: 0.0901

The information below is about J3_4LFB_009

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_37047.6

Basepair signature

cWW-cSS-tHW-F-F-F-cWW-cWW-F-cSH-F-F

Number of instances in this motif group

4

Unit IDs

5HCQ|1|2a|C|1219
5HCQ|1|2a|A|1220
5HCQ|1|2a|A|1221
5HCQ|1|2a|U|1222
5HCQ|1|2a|G|1223
*
5HCQ|1|2a|C|1278
5HCQ|1|2a|C|1279
5HCQ|1|2a|C|1280
5HCQ|1|2a|A|1281
5HCQ|1|2a|G|1282
5HCQ|1|2a|U|1283
5HCQ|1|2a|U|1284
5HCQ|1|2a|C|1285
*
5HCQ|1|2a|G|1316
5HCQ|1|2a|C|1317
5HCQ|1|2a|C|1318
5HCQ|1|2a|G|1319

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2g

30S ribosomal protein S7

Chain 2m

30S ribosomal protein S13

Chain 2u

30S ribosomal protein Thx