J4_5HD1_029

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

GAG*CAUGUG*CAAAG*CGC

Length

17 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

J4_5HD1_029 not in the Motif Atlas

Homologous match to J4_4LFB_002

Geometric discrepancy: 0.1496

The information below is about J4_4LFB_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_88771.1

Basepair signature

cWW-tSS-cWW-tSS-cWW-cWW-tWH-tWH-cSH-cWW

Number of instances in this motif group

1

Unit IDs

5HD1|1|1a|G|137
5HD1|1|1a|A|138
5HD1|1|1a|G|139
*
5HD1|1|1a|C|173
5HD1|1|1a|A|174
5HD1|1|1a|U|175
5HD1|1|1a|G|176
5HD1|1|1a|U|177
5HD1|1|1a|G|178
*
5HD1|1|1a|C|201
5HD1|1|1a|A|202
5HD1|1|1a|A|203
5HD1|1|1a|A|204
5HD1|1|1a|G|205
*
5HD1|1|1a|C|215
5HD1|1|1a|G|216
5HD1|1|1a|C|217

Current chains

Chain 1a

16S Ribosomal RNA

Nearby chains

Chain 1t

30S ribosomal protein S20