HL_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

GUGAAAGCC

Length

9 nucleotides

Bulged bases

5FDV|1|1A|G|353, 5FDV|1|1A|A|354, 5FDV|1|1A|A|355

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_011 not in the Motif Atlas

Homologous match to HL_7RQB_012

Geometric discrepancy: 0.0526

The information below is about HL_7RQB_012

Detailed Annotation

T-loop with unstacked turn

Broad Annotation

T-loop

Motif group

HL_08002.9

Basepair signature

cWW-tWH-F-F

Number of instances in this motif group

19

Unit IDs

5FDV|1|1A|G|351
5FDV|1|1A|U|352
5FDV|1|1A|G|353
5FDV|1|1A|A|354
5FDV|1|1A|A|355
5FDV|1|1A|A|356
5FDV|1|1A|G|357
5FDV|1|1A|C|358
5FDV|1|1A|C|359

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 1F

50S ribosomal protein L4

Chain 1Y

50S ribosomal protein L24