J3_5HCQ_025

3D structure

PDB id

5HCQ (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of antimicrobial peptide Oncocin d15-19 bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

CUAG*CGAAG*CGUUAAG

Length

16 nucleotides

Bulged bases

5HCQ|1|2a|U|849

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_5HCQ_025 not in the Motif Atlas

Homologous match to J3_4LFB_001

Geometric discrepancy: 0.0708

The information below is about J3_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_85054.4

Basepair signature

cWW-tWW-tHS-F-cWW-tHS-cWW-F

Number of instances in this motif group

3

Unit IDs

5HCQ|1|2a|C|810
5HCQ|1|2a|U|811
5HCQ|1|2a|A|812
5HCQ|1|2a|G|813
*
5HCQ|1|2a|C|835
5HCQ|1|2a|G|836
5HCQ|1|2a|A|837
5HCQ|1|2a|A|838
5HCQ|1|2a|G|839
*
5HCQ|1|2a|C|846
5HCQ|1|2a|G|847
5HCQ|1|2a|U|848
5HCQ|1|2a|U|849
5HCQ|1|2a|A|850
5HCQ|1|2a|A|851
5HCQ|1|2a|G|852

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2b

30S ribosomal protein S2

Chain 2h

30S ribosomal protein S8