3D structure

PDB id
8K2D (explore in PDB, NAKB, or RNA 3D Hub)
Description
Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A
Experimental method
ELECTRON MICROSCOPY
Resolution
3.2 Å

Loop

Sequence
CACUG*CGUGCUGG*CGAG
Length
17 nucleotides
Bulged bases
8K2D|1|C2|U|1473, 8K2D|1|C2|G|1539
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_8K2D_021 not in the Motif Atlas
Homologous match to J3_4V88_041
Geometric discrepancy: 0.2205
The information below is about J3_4V88_041
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J3_37047.3
Basepair signature
cWW-cSS-cSH-F-tWH-F-cWW-cSH-F-F-F-cWW
Number of instances in this motif group
5

Unit IDs

8K2D|1|C2|C|1470
8K2D|1|C2|A|1471
8K2D|1|C2|C|1472
8K2D|1|C2|U|1473
8K2D|1|C2|G|1474
*
8K2D|1|C2|C|1533
8K2D|1|C2|G|1534
8K2D|1|C2|U|1535
8K2D|1|C2|G|1536
8K2D|1|C2|C|1537
8K2D|1|C2|U|1538
8K2D|1|C2|G|1539
8K2D|1|C2|G|1540
*
8K2D|1|C2|C|1571
8K2D|1|C2|G|1572
8K2D|1|C2|A|1573
8K2D|1|C2|G|1574

Current chains

Chain C2
18S rRNA

Nearby chains

Chain SF
Small ribosomal subunit protein uS7
Chain SS
Small ribosomal subunit protein uS13A
Chain ST
Small ribosomal subunit protein eS19A
Chain SZ
Small ribosomal subunit protein eS25A

Coloring options:


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