J4_4YPB_006

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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

4YPB|1|RA|U|405

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_4YPB_006 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.1332

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_45801.6

Basepair signature

cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-F-cWW

Number of instances in this motif group

7

Unit IDs

4YPB|1|RA|C|268
4YPB|1|RA|U|269
*
4YPB|1|RA|G|370
4YPB|1|RA|A|371
4YPB|1|RA|G|372
4YPB|1|RA|U|373
4YPB|1|RA|A|374
4YPB|1|RA|C|375
*
4YPB|1|RA|G|399
4YPB|1|RA|G|400
4YPB|1|RA|A|401
4YPB|1|RA|A|402
4YPB|1|RA|U|403
4YPB|1|RA|C|404
4YPB|1|RA|U|405
4YPB|1|RA|G|406
*
4YPB|1|RA|U|421
4YPB|1|RA|A|422
4YPB|1|RA|A|423
4YPB|1|RA|G|424

Current chains

Chain RA

23S rRNA

Nearby chains

Chain R1

50S ribosomal protein L28

Chain RI

50S ribosomal protein L9