J5_5HCQ_009

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

CAAG*CGGACGGG*CAG*CAC*GGCAG

Length

23 nucleotides

Bulged bases

5HCQ|1|1a|A|103, 5HCQ|1|1a|C|348

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

J5_5HCQ_009 not in the Motif Atlas

Homologous match to J5_6CZR_021

Geometric discrepancy: 0.0854

The information below is about J5_6CZR_021

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_59910.5

Basepair signature

cWW-F-tSS-cSS-F-cWW-cWW-cWW-F-F-cWW-F-F-cWW-cWW

Number of instances in this motif group

5

Unit IDs

5HCQ|1|1a|C|59
5HCQ|1|1a|A|60
5HCQ|1|1a|A|61
5HCQ|1|1a|G|62
*
5HCQ|1|1a|C|100
5HCQ|1|1a|G|101
5HCQ|1|1a|G|102
5HCQ|1|1a|A|103
5HCQ|1|1a|C|104
5HCQ|1|1a|G|105
5HCQ|1|1a|G|106
5HCQ|1|1a|G|107
*
5HCQ|1|1a|C|310
5HCQ|1|1a|A|311
5HCQ|1|1a|G|312
*
5HCQ|1|1a|C|333
5HCQ|1|1a|A|334
5HCQ|1|1a|C|335
*
5HCQ|1|1a|G|346
5HCQ|1|1a|G|347
5HCQ|1|1a|C|348
5HCQ|1|1a|A|349
5HCQ|1|1a|G|350

Current chains

Chain 1a

16S Ribosomal RNA

Nearby chains

Chain 1O

50S ribosomal protein L14

Chain 1T

50S ribosomal protein L19

Chain 1p

30S ribosomal protein S16

Chain 1t

30S ribosomal protein S20