IL_5FDV_051

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

GCAAUG*CAGC

Length

10 nucleotides

Bulged bases

5FDV|1|1A|G|1378

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_5FDV_051 not in the Motif Atlas

Geometric match to IL_4V88_408

Geometric discrepancy: 0.3702

The information below is about IL_4V88_408

Detailed Annotation

C-loop with extra cWW pair

Broad Annotation

C-loop

Motif group

IL_11347.2

Basepair signature

cWW-cWW-L-cWW-L

Number of instances in this motif group

3

Unit IDs

5FDV|1|1A|G|1365
5FDV|1|1A|C|1366
5FDV|1|1A|A|1367
5FDV|1|1A|A|1368
5FDV|1|1A|U|1369
5FDV|1|1A|G|1370
*
5FDV|1|1A|C|1376
5FDV|1|1A|A|1377
5FDV|1|1A|G|1378
5FDV|1|1A|C|1379

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 1W

50S ribosomal protein L22

Chain 1X

50S ribosomal protein L23