J3_5HD1_070

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

CGC*GGACUGC*GAGGAAGGAG

Length

20 nucleotides

Bulged bases

5HD1|1|2a|A|1165

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_070 not in the Motif Atlas

Homologous match to J3_4LFB_018

Geometric discrepancy: 0.1637

The information below is about J3_4LFB_018

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_40706.1

Basepair signature

cWW-F-cHW-cWW-tWH-cWW-F-tSW-tWS-cSH-cWW-cWW

Number of instances in this motif group

2

Unit IDs

5HD1|1|2a|C|1099
5HD1|1|2a|G|1100
5HD1|1|2a|C|1101
*
5HD1|1|2a|G|1138
5HD1|1|2a|G|1139
5HD1|1|2a|A|1140
5HD1|1|2a|C|1141
5HD1|1|2a|U|1142
5HD1|1|2a|G|1143
5HD1|1|2a|C|1144
*
5HD1|1|2a|G|1157
5HD1|1|2a|A|1158
5HD1|1|2a|G|1159
5HD1|1|2a|G|1160
5HD1|1|2a|A|1161
5HD1|1|2a|A|1162
5HD1|1|2a|G|1163
5HD1|1|2a|G|1164
5HD1|1|2a|A|1165
5HD1|1|2a|G|1166

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2b

30S ribosomal protein S2

Chain 2i

30S ribosomal protein S9

Chain 2n

30S ribosomal protein S14 type Z