J7_5FDV_003

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

AUGGUAAG*UACAAGC*GAACUG*CUAC*GCGCAG*CC*GU

Length

35 nucleotides

Bulged bases

5FDV|1|2A|G|530, 5FDV|1|2A|C|2021

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|A|8
5FDV|1|2A|U|9
5FDV|1|2A|G|10
5FDV|1|2A|G|11
5FDV|1|2A|U|12
5FDV|1|2A|A|13
5FDV|1|2A|A|14
5FDV|1|2A|G|15
*
5FDV|1|2A|U|525
5FDV|1|2A|A|526
5FDV|1|2A|C|527
5FDV|1|2A|A|528
5FDV|1|2A|A|529
5FDV|1|2A|G|530
5FDV|1|2A|C|531
*
5FDV|1|2A|G|2018
5FDV|1|2A|A|2019
5FDV|1|2A|A|2020
5FDV|1|2A|C|2021
5FDV|1|2A|U|2022
5FDV|1|2A|G|2023
*
5FDV|1|2A|C|2040
5FDV|1|2A|U|2041
5FDV|1|2A|A|2042
5FDV|1|2A|C|2043
*
5FDV|1|2A|G|2625
5FDV|1|2A|C|2626
5FDV|1|2A|G|2627
5FDV|1|2A|C|2628
5FDV|1|2A|A|2629
5FDV|1|2A|G|2630
*
5FDV|1|2A|C|2788
5FDV|1|2A|C|2789
*
5FDV|1|2A|G|2894
5FDV|1|2A|U|2895

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 25

50S ribosomal protein L32

Chain 2E

50S ribosomal protein L3

Chain 2N

50S ribosomal protein L13

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22