HL_5FDV_114

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|2A|G|329, 5FDV|1|2A|A|330, 5FDV|1|2A|A|331

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_114 not in the Motif Atlas

Homologous match to HL_7RQB_012

Geometric discrepancy: 0.0592

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|2A|G|327
5FDV|1|2A|U|328
5FDV|1|2A|G|329
5FDV|1|2A|A|330
5FDV|1|2A|A|331
5FDV|1|2A|A|332
5FDV|1|2A|G|333
5FDV|1|2A|C|334
5FDV|1|2A|C|335

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2F

50S ribosomal protein L4

Chain 2Y

50S ribosomal protein L24