IL_5NDK_367

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

GCGUAGGAUAGGUGGGAGCC*GGCGCCGGUGAAAUACCACCC

Length

41 nucleotides

Bulged bases

5NDK|1|1H|C|2136, 5NDK|1|1H|U|2138, 5NDK|1|1H|G|2191, 5NDK|1|1H|U|2192, 5NDK|1|1H|A|2195

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

5NDK|1|1H|G|2135
5NDK|1|1H|C|2136
5NDK|1|1H|G|2137
5NDK|1|1H|U|2138
5NDK|1|1H|A|2139
5NDK|1|1H|G|2140
5NDK|1|1H|G|2141
5NDK|1|1H|A|2142
5NDK|1|1H|U|2143
5NDK|1|1H|A|2144
5NDK|1|1H|G|2145
5NDK|1|1H|G|2146
5NDK|1|1H|U|2147
5NDK|1|1H|G|2148
5NDK|1|1H|G|2149
5NDK|1|1H|G|2150
5NDK|1|1H|A|2151
5NDK|1|1H|G|2152
5NDK|1|1H|C|2153
5NDK|1|1H|C|2154
*
5NDK|1|1H|G|2184
5NDK|1|1H|G|2185
5NDK|1|1H|C|2186
5NDK|1|1H|G|2187
5NDK|1|1H|C|2188
5NDK|1|1H|C|2189
5NDK|1|1H|G|2190
5NDK|1|1H|G|2191
5NDK|1|1H|U|2192
5NDK|1|1H|G|2193
5NDK|1|1H|A|2194
5NDK|1|1H|A|2195
5NDK|1|1H|A|2196
5NDK|1|1H|U|2197
5NDK|1|1H|A|2198
5NDK|1|1H|C|2199
5NDK|1|1H|C|2200
5NDK|1|1H|A|2201
5NDK|1|1H|C|2202
5NDK|1|1H|C|2203
5NDK|1|1H|C|2204

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain V1

Transfer RNA; tRNA