J3_5HD1_031

3D structure

PDB id

5HD1 (explore in PDB, NAKB, or RNA 3D Hub)

Description

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

Experimental method

X-RAY DIFFRACTION

Resolution

2.7 Å

Loop

Sequence

CAAUG*CCCAGUUC*GCCG

Length

17 nucleotides

Bulged bases

5HD1|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_5HD1_031 not in the Motif Atlas

Homologous match to J3_4LFB_009

Geometric discrepancy: 0.0963

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

5HD1|1|2a|C|1219
5HD1|1|2a|A|1220
5HD1|1|2a|A|1221
5HD1|1|2a|U|1222
5HD1|1|2a|G|1223
*
5HD1|1|2a|C|1278
5HD1|1|2a|C|1279
5HD1|1|2a|C|1280
5HD1|1|2a|A|1281
5HD1|1|2a|G|1282
5HD1|1|2a|U|1283
5HD1|1|2a|U|1284
5HD1|1|2a|C|1285
*
5HD1|1|2a|G|1316
5HD1|1|2a|C|1317
5HD1|1|2a|C|1318
5HD1|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