3D structure

PDB id
5NDJ (explore in PDB, NAKB, or RNA 3D Hub)
Description
Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)
Experimental method
X-RAY DIFFRACTION
Resolution
3.15 Å

Loop

Sequence
GGAGUACG*UGAAAC
Length
14 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
IL_5NDJ_034 not in the Motif Atlas
Homologous match to IL_4LFB_034
Geometric discrepancy: 0.0684
The information below is about IL_4LFB_034
Detailed Annotation
8x6 Sarcin-Ricin with inserted Y; G-bulge
Broad Annotation
Sarcin-Ricin; G-bulge
Motif group
IL_41756.4
Basepair signature
cWW-tSH-tHH-cSH-tWH-tHS-cWW-L
Number of instances in this motif group
4

Unit IDs

5NDJ|1|13|G|1510
5NDJ|1|13|G|1511
5NDJ|1|13|A|1512
5NDJ|1|13|G|1513
5NDJ|1|13|U|1514
5NDJ|1|13|A|1515
5NDJ|1|13|C|1516
5NDJ|1|13|G|1517
*
5NDJ|1|13|U|1528
5NDJ|1|13|G|1529
5NDJ|1|13|A|1530
5NDJ|1|13|A|1531
5NDJ|1|13|A|1532
5NDJ|1|13|C|1533

Current chains

Chain 13
16S ribosomal RNA

Nearby chains

Chain 3I
30S ribosomal protein S12
Chain 8I
30S ribosomal protein S17

Coloring options:


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