IL_5HD1_267

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

AUC*GGUUU

Length

8 nucleotides

Bulged bases

5HD1|1|2A|U|2502

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_267 not in the Motif Atlas

Homologous match to IL_7RQB_094

Geometric discrepancy: 0.0898

The information below is about IL_7RQB_094

Detailed Annotation

Major groove minor groove platform with extra cWW

Broad Annotation

Major groove minor groove platform; mini C-loop

Motif group

IL_92788.2

Basepair signature

cWW-L-R-L-cWW-L

Number of instances in this motif group

14

Unit IDs

5HD1|1|2A|A|2470
5HD1|1|2A|U|2471
5HD1|1|2A|C|2472
*
5HD1|1|2A|G|2500
5HD1|1|2A|G|2501
5HD1|1|2A|U|2502
5HD1|1|2A|U|2503
5HD1|1|2A|U|2504

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2Q

50S ribosomal protein L16

Chain 2z

Pyrrhocoricin