J3_5HCQ_056

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

CGAAG*CGCCAGAGAG*CGUAG

Length

20 nucleotides

Bulged bases

5HCQ|1|2A|G|344

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_056 not in the Motif Atlas

Homologous match to J3_9DFE_006

Geometric discrepancy: 0.0636

The information below is about J3_9DFE_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_46299.2

Basepair signature

cWW-F-F-F-cHH-cWW-tHS-F-cWW-cSW-tHS-cWW

Number of instances in this motif group

3

Unit IDs

5HCQ|1|2A|C|320
5HCQ|1|2A|G|321
5HCQ|1|2A|A|322
5HCQ|1|2A|A|323
5HCQ|1|2A|G|324
*
5HCQ|1|2A|C|339
5HCQ|1|2A|G|340
5HCQ|1|2A|C|341
5HCQ|1|2A|C|342
5HCQ|1|2A|A|343
5HCQ|1|2A|G|344
5HCQ|1|2A|A|345
5HCQ|1|2A|G|346
5HCQ|1|2A|A|347
5HCQ|1|2A|G|348
*
5HCQ|1|2A|C|360
5HCQ|1|2A|G|361
5HCQ|1|2A|U|362
5HCQ|1|2A|A|363
5HCQ|1|2A|G|364

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2F

50S ribosomal protein L4

Chain 2Y

50S ribosomal protein L24