IL_5NDJ_311

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

GCGUAGGAUAG*CC

Length

13 nucleotides

Bulged bases

5NDJ|1|1H|C|2136, 5NDJ|1|1H|G|2137

QA status

Unknown status

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_311 not in the Motif Atlas

Geometric match to IL_1KXK_003

Geometric discrepancy: 0.3552

The information below is about IL_1KXK_003

Detailed Annotation

Multiple bulged bases

Broad Annotation

No text annotation

Motif group

IL_42626.2

Basepair signature

cWW-cWW

Number of instances in this motif group

14

Unit IDs

5NDJ|1|1H|G|2135
5NDJ|1|1H|C|2136
5NDJ|1|1H|G|2137
5NDJ|1|1H|U|2138
5NDJ|1|1H|A|2139
5NDJ|1|1H|G|2140
5NDJ|1|1H|G|2141
5NDJ|1|1H|A|2142
5NDJ|1|1H|U|2143
5NDJ|1|1H|A|2144
5NDJ|1|1H|G|2145
*
5NDJ|1|1H|C|2203
5NDJ|1|1H|C|2204

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain V1

Transfer RNA; tRNA