IL_5HD1_175

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

CGGGAG*CAG

Length

9 nucleotides

Bulged bases

5HD1|1|1a|G|1426

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

IL_5HD1_175 not in the Motif Atlas

Homologous match to IL_6CZR_172

Geometric discrepancy: 0.2407

The information below is about IL_6CZR_172

Detailed Annotation

Isolated basepair with bulged bases

Broad Annotation

Isolated basepair with bulged bases

Motif group

IL_97255.3

Basepair signature

cWW-tSH-L-cWW-L

Number of instances in this motif group

5

Unit IDs

5HD1|1|1a|C|1423
5HD1|1|1a|G|1424
5HD1|1|1a|G|1425
5HD1|1|1a|G|1426
5HD1|1|1a|A|1427
5HD1|1|1a|G|1428
*
5HD1|1|1a|C|1437
5HD1|1|1a|A|1438
5HD1|1|1a|G|1439

Current chains

Chain 1a

16S Ribosomal RNA

Nearby chains

Chain 1A

Large subunit ribosomal RNA; LSU rRNA

Chain 1T

50S ribosomal protein L19

Chain 1t

30S ribosomal protein S20