J4_5HCQ_018

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

GGUUC*GGUUAG*CU*ACCCGUAC

Length

21 nucleotides

Bulged bases

5HCQ|1|2A|U|1386

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_018 not in the Motif Atlas

Homologous match to J4_9DFE_004

Geometric discrepancy: 0.0625

The information below is about J4_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_69051.6

Basepair signature

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

Number of instances in this motif group

7

Unit IDs

5HCQ|1|2A|G|1355
5HCQ|1|2A|G|1356
5HCQ|1|2A|U|1357
5HCQ|1|2A|U|1358
5HCQ|1|2A|C|1359
*
5HCQ|1|2A|G|1383
5HCQ|1|2A|G|1384
5HCQ|1|2A|U|1385
5HCQ|1|2A|U|1386
5HCQ|1|2A|A|1387
5HCQ|1|2A|G|1388
*
5HCQ|1|2A|C|1449
5HCQ|1|2A|U|1450
*
5HCQ|1|2A|A|1642
5HCQ|1|2A|C|1643
5HCQ|1|2A|C|1644
5HCQ|1|2A|C|1645
5HCQ|1|2A|G|1646
5HCQ|1|2A|U|1647
5HCQ|1|2A|A|1648
5HCQ|1|2A|C|1649

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 27

50S ribosomal protein L34

Chain 2X

50S ribosomal protein L23