J3_5HD1_038

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

GCGGGAC*GGCAG*CC

Length

14 nucleotides

Bulged bases

5HD1|1|1A|A|1429

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_038 not in the Motif Atlas

Homologous match to J3_9DFE_012

Geometric discrepancy: 0.0705

The information below is about J3_9DFE_012

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_31965.2

Basepair signature

cWW-F-cWW-F-F-F-F-F-cWW-F

Number of instances in this motif group

6

Unit IDs

5HD1|1|1A|G|1389
5HD1|1|1A|C|1390
5HD1|1|1A|G|1391
5HD1|1|1A|G|1392
5HD1|1|1A|G|1393
5HD1|1|1A|A|1394
5HD1|1|1A|C|1395
*
5HD1|1|1A|G|1426
5HD1|1|1A|G|1427
5HD1|1|1A|C|1428
5HD1|1|1A|A|1429
5HD1|1|1A|G|1430
*
5HD1|1|1A|C|1447
5HD1|1|1A|C|1448

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 17

50S ribosomal protein L34

Chain 1X

50S ribosomal protein L23