IL_5HD1_280

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

GAUAAC*GGAAGC

Length

12 nucleotides

Bulged bases

5HD1|1|2A|A|2777

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_280 not in the Motif Atlas

Homologous match to IL_5J7L_350

Geometric discrepancy: 0.1427

The information below is about IL_5J7L_350

Detailed Annotation

UAA/GAN with extra cWW

Broad Annotation

No text annotation

Motif group

IL_49767.8

Basepair signature

cWW-cWW-tWH-L-tHS-cWW

Number of instances in this motif group

6

Unit IDs

5HD1|1|2A|G|2749
5HD1|1|2A|A|2750
5HD1|1|2A|U|2751
5HD1|1|2A|A|2752
5HD1|1|2A|A|2753
5HD1|1|2A|C|2754
*
5HD1|1|2A|G|2774
5HD1|1|2A|G|2775
5HD1|1|2A|A|2776
5HD1|1|2A|A|2777
5HD1|1|2A|G|2778
5HD1|1|2A|C|2779

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 29

50S ribosomal protein L36

Chain 2H

50S ribosomal protein L6

Chain 2N

50S ribosomal protein L13