IL_5NDK_143

3D structure

PDB id

5NDK (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

Experimental method

X-RAY DIFFRACTION

Resolution

2.95 Å

Loop

Sequence

GCGUAGGAUAGG*CCC

Length

15 nucleotides

Bulged bases

5NDK|1|14|U|2138, 5NDK|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_5NDK_143 not in the Motif Atlas

Geometric match to IL_4V88_406

Geometric discrepancy: 0.2833

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

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