IL_5NDJ_106

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

AUGAGUAA*UGAAAUU

Length

15 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_106 not in the Motif Atlas

Homologous match to IL_7RQB_049

Geometric discrepancy: 0.0483

The information below is about IL_7RQB_049

Detailed Annotation

8x7 Sarcin-Ricin; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_04346.7

Basepair signature

cWW-cWW-tSH-tHH-cSH-tWH-tHS-cWW

Number of instances in this motif group

15

Unit IDs

5NDJ|1|14|A|1311
5NDJ|1|14|U|1312
5NDJ|1|14|G|1313
5NDJ|1|14|A|1314
5NDJ|1|14|G|1315
5NDJ|1|14|U|1316
5NDJ|1|14|A|1317
5NDJ|1|14|A|1318
*
5NDJ|1|14|U|2036
5NDJ|1|14|G|2037
5NDJ|1|14|A|2038
5NDJ|1|14|A|2039
5NDJ|1|14|A|2040
5NDJ|1|14|U|2041
5NDJ|1|14|U|2042

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 39

50S ribosomal protein L4

Chain A5

50S ribosomal protein L22

Chain J5

50S ribosomal protein L32