IL_5HD1_088

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

UGA*UG

Length

5 nucleotides

Bulged bases

None detected

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_088 not in the Motif Atlas

Geometric match to IL_4WF9_091

Geometric discrepancy: 0.123

The information below is about IL_4WF9_091

Detailed Annotation

Major groove platform

Broad Annotation

No text annotation

Motif group

IL_48076.6

Basepair signature

cWW-cSH-cWW

Number of instances in this motif group

41

Unit IDs

5HD1|1|1A|U|2468
5HD1|1|1A|G|2469
5HD1|1|1A|A|2470
*
5HD1|1|1A|U|2504
5HD1|1|1A|G|2505

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1Q

50S ribosomal protein L16

Chain 1z

Pyrrhocoricin