IL_5HCQ_028

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

GCACU*AAAC

Length

9 nucleotides

Bulged bases

None detected

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

IL_5HCQ_028 not in the Motif Atlas

Homologous match to IL_7RQB_029

Geometric discrepancy: 0.0473

The information below is about IL_7RQB_029

Detailed Annotation

C-loop with bulged stacked A's

Broad Annotation

C-loop

Motif group

IL_02509.1

Basepair signature

cWW-tSW-cWS-cSH-tWH-R-R-cWW

Number of instances in this motif group

5

Unit IDs

5HCQ|1|1A|G|910
5HCQ|1|1A|C|911
5HCQ|1|1A|A|912
5HCQ|1|1A|C|913
5HCQ|1|1A|U|914
*
5HCQ|1|1A|A|954
5HCQ|1|1A|A|955
5HCQ|1|1A|A|956
5HCQ|1|1A|C|957

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1B

5S ribosomal RNA; 5S rRNA

Chain 1Q

50S ribosomal protein L16

Chain 1Z

50S ribosomal protein L25