HL_5FDV_099

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

CUGCAACCCG

Length

10 nucleotides

Bulged bases

None detected

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

HL_5FDV_099 not in the Motif Atlas

Homologous match to HL_4LFB_029

Geometric discrepancy: 0.1292

The information below is about HL_4LFB_029

Detailed Annotation

T-loop with 3 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_02887.3

Basepair signature

cWW-tWH-F-F-F-F-F-F

Number of instances in this motif group

2

Unit IDs

5FDV|1|1a|C|1314
5FDV|1|1a|U|1315
5FDV|1|1a|G|1316
5FDV|1|1a|C|1317
5FDV|1|1a|A|1318
5FDV|1|1a|A|1319
5FDV|1|1a|C|1320
5FDV|1|1a|C|1321
5FDV|1|1a|C|1322
5FDV|1|1a|G|1323

Current chains

Chain 1a

16S ribosomal RNA

Nearby chains

Chain 1m

30S ribosomal protein S13

Chain 1n

30S ribosomal protein S14 type Z

Chain 1s

30S ribosomal protein S19