J5_5FDV_010

3D structure

PDB id

5FDV (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Pyrrhocoricin antimicrobial peptide 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

5FDV|1|2A|U|50

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_5FDV_010 not in the Motif Atlas

Homologous match to J5_9DFE_001

Geometric discrepancy: 0.047

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

5FDV|1|2A|C|47
5FDV|1|2A|G|48
5FDV|1|2A|A|49
5FDV|1|2A|U|50
5FDV|1|2A|G|51
5FDV|1|2A|A|52
5FDV|1|2A|A|53
5FDV|1|2A|G|54
*
5FDV|1|2A|C|116
5FDV|1|2A|G|117
5FDV|1|2A|A|118
5FDV|1|2A|A|119
5FDV|1|2A|U|120
5FDV|1|2A|G|121
*
5FDV|1|2A|C|130
5FDV|1|2A|G|131
*
5FDV|1|2A|C|148
5FDV|1|2A|A|149
5FDV|1|2A|C|150
*
5FDV|1|2A|G|176
5FDV|1|2A|G|177
5FDV|1|2A|G|178

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 27

50S ribosomal protein L34

Chain 2X

50S ribosomal protein L23