J3_5HD1_068

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

CUUGACAU*ACAG*CUUACG

Length

18 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

J3_5HD1_068 not in the Motif Atlas

Homologous match to J3_4LFB_016

Geometric discrepancy: 0.1679

The information below is about J3_4LFB_016

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_76475.2

Basepair signature

cWW-tWH-F-tHS-cWW-cWW-F-cWS-cWS-cWW

Number of instances in this motif group

2

Unit IDs

5HD1|1|2a|C|968
5HD1|1|2a|U|969
5HD1|1|2a|U|970
5HD1|1|2a|G|971
5HD1|1|2a|A|972
5HD1|1|2a|C|973
5HD1|1|2a|A|974
5HD1|1|2a|U|975
*
5HD1|1|2a|A|1027
5HD1|1|2a|C|1028
5HD1|1|2a|A|1029
5HD1|1|2a|G|1030
*
5HD1|1|2a|C|1192
5HD1|1|2a|U|1193
5HD1|1|2a|U|1194
5HD1|1|2a|A|1195
5HD1|1|2a|C|1196
5HD1|1|2a|G|1197

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2c

30S ribosomal protein S3

Chain 2n

30S ribosomal protein S14 type Z