IL_5NDJ_142

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

GCGUAGGAUAGG*CCC

Length

15 nucleotides

Bulged bases

5NDJ|1|14|U|2138, 5NDJ|1|14|A|2144

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_142 not in the Motif Atlas

Geometric match to IL_4V88_406

Geometric discrepancy: 0.2942

The information below is about IL_4V88_406

Detailed Annotation

Isolated near basepair

Broad Annotation

Isolated near basepair

Motif group

IL_76004.2

Basepair signature

cWW-L-R-cWW

Number of instances in this motif group

18

Unit IDs

5NDJ|1|14|G|2135
5NDJ|1|14|C|2136
5NDJ|1|14|G|2137
5NDJ|1|14|U|2138
5NDJ|1|14|A|2139
5NDJ|1|14|G|2140
5NDJ|1|14|G|2141
5NDJ|1|14|A|2142
5NDJ|1|14|U|2143
5NDJ|1|14|A|2144
5NDJ|1|14|G|2145
5NDJ|1|14|G|2146
*
5NDJ|1|14|C|2202
5NDJ|1|14|C|2203
5NDJ|1|14|C|2204

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 13

Small subunit ribosomal RNA; SSU rRNA

Chain V4

Transfer RNA; tRNA