3D structure

PDB id
5ND8 (explore in PDB, NAKB, or RNA 3D Hub)
Description
Hibernating ribosome from Staphylococcus aureus (Unrotated state)
Experimental method
ELECTRON MICROSCOPY
Resolution
3.7 Å

Loop

Sequence
GC*GUGAAAAGCAC*GAGUGAAAUAGAACC
Length
28 nucleotides
Bulged bases
5ND8|1|A|U|549, 5ND8|1|A|A|553
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_5ND8_026 not in the Motif Atlas
Homologous match to J3_4WF9_011
Geometric discrepancy: 0.1394
The information below is about J3_4WF9_011
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J3_92134.2
Basepair signature
cWW-cWW-cWW-F-tWH-cSS-tSS-tSH-tSH-tWW-tHH-tWH-tWW-F-F-cSS-cSW-F-tHS-cWW
Number of instances in this motif group
6

Unit IDs

5ND8|1|A|G|30
5ND8|1|A|C|31
*
5ND8|1|A|G|520
5ND8|1|A|U|521
5ND8|1|A|G|522
5ND8|1|A|A|523
5ND8|1|A|A|524
5ND8|1|A|A|525
5ND8|1|A|A|526
5ND8|1|A|G|527
5ND8|1|A|C|528
5ND8|1|A|A|529
5ND8|1|A|C|530
*
5ND8|1|A|G|541
5ND8|1|A|A|542
5ND8|1|A|G|543
5ND8|1|A|U|544
5ND8|1|A|G|545
5ND8|1|A|A|546
5ND8|1|A|A|547
5ND8|1|A|A|548
5ND8|1|A|U|549
5ND8|1|A|A|550
5ND8|1|A|G|551
5ND8|1|A|A|552
5ND8|1|A|A|553
5ND8|1|A|C|554
5ND8|1|A|C|555

Current chains

Chain A
23S ribosomal RNA

Nearby chains

Chain T
50S ribosomal protein L20
Chain V
50S ribosomal protein L22
Chain X
50S ribosomal protein L24

Coloring options:


Copyright 2025 BGSU RNA group. Page generated in 0.1888 s