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
UUUA*UUUG*CG*CG*CGGAUAAAA
Length
21 nucleotides
Bulged bases
4YPB|1|YA|U|2076, 4YPB|1|YA|G|2428, 4YPB|1|YA|G|2429, 4YPB|1|YA|A|2430, 4YPB|1|YA|U|2431
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_019 not in the Motif Atlas
Homologous match to J5_9DFE_007
Geometric discrepancy: 0.0635
The information below is about J5_9DFE_007
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J5_39529.1
Basepair signature
cWW-cWH-cWH-F-cWW-F-F-cWW-F-cWW-cWW
Number of instances in this motif group
3

Unit IDs

4YPB|1|YA|U|2074
4YPB|1|YA|U|2075
4YPB|1|YA|U|2076
4YPB|1|YA|A|2077
*
4YPB|1|YA|U|2243
4YPB|1|YA|U|2244
4YPB|1|YA|U|2245
4YPB|1|YA|G|2246
*
4YPB|1|YA|C|2258
4YPB|1|YA|G|2259
*
4YPB|1|YA|C|2281
4YPB|1|YA|G|2282
*
4YPB|1|YA|C|2427
4YPB|1|YA|G|2428
4YPB|1|YA|G|2429
4YPB|1|YA|A|2430
4YPB|1|YA|U|2431
4YPB|1|YA|A|2432
4YPB|1|YA|A|2433
4YPB|1|YA|A|2434
4YPB|1|YA|A|2435

Current chains

Chain YA
23S rRNA

Nearby chains

Chain XW
Transfer RNA; tRNA
Chain Y0
50S ribosomal protein L27
Chain Y1
50S ribosomal protein L28
Chain Y6
50S ribosomal protein L33
Chain YD
50S ribosomal protein L2
Chain YP
50S ribosomal protein L15

Coloring options:


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