IL_5HD1_246

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

UGCGAAC*GGAGGUAUA

Length

16 nucleotides

Bulged bases

5HD1|1|2A|G|1831, 5HD1|1|2A|G|1846, 5HD1|1|2A|U|1850

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_246 not in the Motif Atlas

Homologous match to IL_7RQB_070

Geometric discrepancy: 0.0486

The information below is about IL_7RQB_070

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_17069.3

Basepair signature

cWW-tSH-tHH-cSS-tWW-tHH-tSS-cWW

Number of instances in this motif group

5

Unit IDs

5HD1|1|2A|U|1828
5HD1|1|2A|G|1829
5HD1|1|2A|C|1830
5HD1|1|2A|G|1831
5HD1|1|2A|A|1832
5HD1|1|2A|A|1833
5HD1|1|2A|C|1834
*
5HD1|1|2A|G|1843
5HD1|1|2A|G|1844
5HD1|1|2A|A|1845
5HD1|1|2A|G|1846
5HD1|1|2A|G|1847
5HD1|1|2A|U|1848
5HD1|1|2A|A|1849
5HD1|1|2A|U|1850
5HD1|1|2A|A|1851

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA