IL_5NDJ_319

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

AUC*GGUUU

Length

8 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_319 not in the Motif Atlas

Geometric match to IL_7RQB_094

Geometric discrepancy: 0.0671

The information below is about IL_7RQB_094

Detailed Annotation

Major groove minor groove platform with extra cWW

Broad Annotation

Major groove minor groove platform; mini C-loop

Motif group

IL_92788.2

Basepair signature

cWW-L-R-L-cWW-L

Number of instances in this motif group

14

Unit IDs

5NDJ|1|1H|A|2474
5NDJ|1|1H|U|2475
5NDJ|1|1H|C|2476
*
5NDJ|1|1H|G|2504
5NDJ|1|1H|G|2505
5NDJ|1|1H|U|2506
5NDJ|1|1H|U|2507
5NDJ|1|1H|U|2508

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 88

50S ribosomal protein L16

Chain I8

50S ribosomal protein L27

Chain W1

Transfer RNA; tRNA