J5_5HCQ_010

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

CGAUGAAG*CGAAUG*CG*CAC*GGG

Length

22 nucleotides

Bulged bases

5HCQ|1|2A|U|48

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

J5_5HCQ_010 not in the Motif Atlas

Homologous match to J5_9DFE_001

Geometric discrepancy: 0.0502

The information below is about J5_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_01737.2

Basepair signature

cWW-F-cWW-F-cWW-tSH-tHH-tHS-cWW-cWW-cWW-F

Number of instances in this motif group

5

Unit IDs

5HCQ|1|2A|C|45
5HCQ|1|2A|G|46
5HCQ|1|2A|A|47
5HCQ|1|2A|U|48
5HCQ|1|2A|G|49
5HCQ|1|2A|A|50
5HCQ|1|2A|A|51
5HCQ|1|2A|G|52
*
5HCQ|1|2A|C|113
5HCQ|1|2A|G|114
5HCQ|1|2A|A|115
5HCQ|1|2A|A|116
5HCQ|1|2A|U|117
5HCQ|1|2A|G|118
*
5HCQ|1|2A|C|127
5HCQ|1|2A|G|128
*
5HCQ|1|2A|C|147
5HCQ|1|2A|A|148
5HCQ|1|2A|C|149
*
5HCQ|1|2A|G|164
5HCQ|1|2A|G|165
5HCQ|1|2A|G|166

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 27

50S ribosomal protein L34

Chain 2X

50S ribosomal protein L23