HL_5HD1_098

3D structure

PDB id

5HD1 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of antimicrobial peptide Pyrrhocoricin bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.7 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_5HD1_098 not in the Motif Atlas

Homologous match to HL_4LFB_029

Geometric discrepancy: 0.1096

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

5HD1|1|1a|C|1296
5HD1|1|1a|U|1297
5HD1|1|1a|G|1298
5HD1|1|1a|C|1299
5HD1|1|1a|A|1300
5HD1|1|1a|A|1301
5HD1|1|1a|C|1302
5HD1|1|1a|C|1303
5HD1|1|1a|C|1304
5HD1|1|1a|G|1305

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