J5_5FDV_011

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

CUAAAC*GGGUCGUG*CGAGUAC*GGAAUCUG*UAAG

Length

33 nucleotides

Bulged bases

5FDV|1|2A|U|272|||A, 5FDV|1|2A|U|405

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

5FDV|1|2A|C|268
5FDV|1|2A|U|269
5FDV|1|2A|A|270
5FDV|1|2A|A|271
5FDV|1|2A|A|271|||A
5FDV|1|2A|C|271|||B
*
5FDV|1|2A|G|271|||V
5FDV|1|2A|G|271|||W
5FDV|1|2A|G|271|||X
5FDV|1|2A|U|271|||Y
5FDV|1|2A|C|271|||Z
5FDV|1|2A|G|272
5FDV|1|2A|U|272|||A
5FDV|1|2A|G|272|||B
*
5FDV|1|2A|C|366
5FDV|1|2A|G|370
5FDV|1|2A|A|371
5FDV|1|2A|G|372
5FDV|1|2A|U|373
5FDV|1|2A|A|374
5FDV|1|2A|C|375
*
5FDV|1|2A|G|399
5FDV|1|2A|G|400
5FDV|1|2A|A|401
5FDV|1|2A|A|402
5FDV|1|2A|U|403
5FDV|1|2A|C|404
5FDV|1|2A|U|405
5FDV|1|2A|G|406
*
5FDV|1|2A|U|421
5FDV|1|2A|A|422
5FDV|1|2A|A|423
5FDV|1|2A|G|424

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 21

50S ribosomal protein L28

Chain 2I

50S ribosomal protein L9