J3_5HCQ_059

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

GCC*GCCUAGUGAACC*GAUCAAC

Length

22 nucleotides

Bulged bases

5HCQ|1|2A|A|2399, 5HCQ|1|2A|U|2401, 5HCQ|1|2A|A|2437

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_059 not in the Motif Atlas

Homologous match to J3_9DFE_015

Geometric discrepancy: 0.0536

The information below is about J3_9DFE_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_20992.1

Basepair signature

cWW-F-F-cWW-tHW-tHW-F-cWW-F-F-F-F-F

Number of instances in this motif group

5

Unit IDs

5HCQ|1|2A|G|2293
5HCQ|1|2A|C|2294
5HCQ|1|2A|C|2295
*
5HCQ|1|2A|G|2395
5HCQ|1|2A|C|2396
5HCQ|1|2A|C|2397
5HCQ|1|2A|U|2398
5HCQ|1|2A|A|2399
5HCQ|1|2A|G|2400
5HCQ|1|2A|U|2401
5HCQ|1|2A|G|2402
5HCQ|1|2A|A|2403
5HCQ|1|2A|A|2404
5HCQ|1|2A|C|2405
5HCQ|1|2A|C|2406
*
5HCQ|1|2A|G|2432
5HCQ|1|2A|A|2433
5HCQ|1|2A|U|2434
5HCQ|1|2A|C|2435
5HCQ|1|2A|A|2436
5HCQ|1|2A|A|2437
5HCQ|1|2A|C|2438

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 20

50S ribosomal protein L27

Chain 21

50S ribosomal protein L28

Chain 26

50S ribosomal protein L33

Chain 28

50S ribosomal protein L35

Chain 2P

50S ribosomal protein L15