J4_5HCQ_015

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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

5HCQ|1|2A|U|431

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

J4_5HCQ_015 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.08

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_45801.6

Basepair signature

cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-F-cWW

Number of instances in this motif group

7

Unit IDs

5HCQ|1|2A|C|256
5HCQ|1|2A|U|257
*
5HCQ|1|2A|G|396
5HCQ|1|2A|A|397
5HCQ|1|2A|G|398
5HCQ|1|2A|U|399
5HCQ|1|2A|A|400
5HCQ|1|2A|C|401
*
5HCQ|1|2A|G|425
5HCQ|1|2A|G|426
5HCQ|1|2A|A|427
5HCQ|1|2A|A|428
5HCQ|1|2A|U|429
5HCQ|1|2A|C|430
5HCQ|1|2A|U|431
5HCQ|1|2A|G|432
*
5HCQ|1|2A|U|447
5HCQ|1|2A|A|448
5HCQ|1|2A|A|449
5HCQ|1|2A|G|450

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 21

50S ribosomal protein L28

Chain 2I

50S ribosomal protein L9