J3_5HD1_016

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

CGAGCUA*UAG*CGAG

Length

14 nucleotides

Bulged bases

5HD1|1|2A|G|732, 5HD1|1|2A|G|838

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

J3_5HD1_016 not in the Motif Atlas

Homologous match to J3_7RQB_004

Geometric discrepancy: 0.0565

The information below is about J3_7RQB_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_39238.4

Basepair signature

cWW-tWH-cWW-tSW-F-F-cWW

Number of instances in this motif group

7

Unit IDs

5HD1|1|2A|C|729
5HD1|1|2A|G|730
5HD1|1|2A|A|731
5HD1|1|2A|G|732
5HD1|1|2A|C|733
5HD1|1|2A|U|734
5HD1|1|2A|A|735
*
5HD1|1|2A|U|819
5HD1|1|2A|A|820
5HD1|1|2A|G|821
*
5HD1|1|2A|C|837
5HD1|1|2A|G|838
5HD1|1|2A|A|839
5HD1|1|2A|G|840

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 27

50S ribosomal protein L34

Chain 2D

50S ribosomal protein L2