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
CUGG*CUUG*CUGAAC*GGUAAUAG*CGAG
Length
26 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
J5_5NDJ_001 not in the Motif Atlas
Homologous match to J5_4LFB_001
Geometric discrepancy: 0.0784
The information below is about J5_4LFB_001
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J5_70703.1
Basepair signature
cWW-F-tWH-F-F-cWW-cWW-cWH-cWH-cWW-tSH-tWH-tHW-tHS-cWW
Number of instances in this motif group
1

Unit IDs

5NDJ|1|13|C|682
5NDJ|1|13|U|683
5NDJ|1|13|G|684
5NDJ|1|13|G|685
*
5NDJ|1|13|C|1044
5NDJ|1|13|U|1045
5NDJ|1|13|U|1046
5NDJ|1|13|G|1047
*
5NDJ|1|13|C|1077
5NDJ|1|13|U|1078
5NDJ|1|13|G|1079
5NDJ|1|13|A|1080
5NDJ|1|13|A|1081
5NDJ|1|13|C|1082
*
5NDJ|1|13|G|1122
5NDJ|1|13|G|1123
5NDJ|1|13|U|1124
5NDJ|1|13|A|1125
5NDJ|1|13|A|1126
5NDJ|1|13|U|1127
5NDJ|1|13|A|1128
5NDJ|1|13|G|1129
*
5NDJ|1|13|C|1174
5NDJ|1|13|G|1175
5NDJ|1|13|A|1176
5NDJ|1|13|G|1177

Current chains

Chain 13
16S ribosomal RNA

Nearby chains

Chain 3E
30S ribosomal protein S4
Chain 3I
30S ribosomal protein S12
Chain 69
50S ribosomal protein L9

Coloring options:


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