J5_4YPB_011

3D structure

PDB id

4YPB (explore in PDB, NAKB, or RNA 3D Hub)

Description

Precleavage 70S structure of the P. vulgaris HigB DeltaH92 toxin bound to the AAA codon

Experimental method

X-RAY DIFFRACTION

Resolution

3.4 Å

Loop

Sequence

CUGG*CUUG*CUGAAC*GGUAAUAG*CGAG

Length

26 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

J5_4YPB_011 not in the Motif Atlas

Homologous match to J5_4LFB_001

Geometric discrepancy: 0.0612

The information below is about J5_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_70703.1

Basepair signature

cWW-F-tWH-F-F-cWW-cWW-cWH-cWH-cWW-tSH-tWH-tHW-tHS-cWW

Number of instances in this motif group

1

Unit IDs

4YPB|1|XA|C|36
4YPB|1|XA|U|37
4YPB|1|XA|G|38
4YPB|1|XA|G|39
*
4YPB|1|XA|C|403
4YPB|1|XA|U|404
4YPB|1|XA|U|405
4YPB|1|XA|G|406
*
4YPB|1|XA|C|436
4YPB|1|XA|U|437
4YPB|1|XA|G|438
4YPB|1|XA|A|439
4YPB|1|XA|A|441
4YPB|1|XA|C|442
*
4YPB|1|XA|G|492
4YPB|1|XA|G|493
4YPB|1|XA|U|494
4YPB|1|XA|A|495
4YPB|1|XA|A|496
4YPB|1|XA|U|498
4YPB|1|XA|A|499
4YPB|1|XA|G|500
*
4YPB|1|XA|C|545
4YPB|1|XA|G|546
4YPB|1|XA|A|547
4YPB|1|XA|G|548

Current chains

Chain XA

16S rRNA

Nearby chains

Chain XD

30S ribosomal protein S4

Chain XL

30S ribosomal protein S12