IL_5NDK_356

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

CUGCGUAGGAUAGGUGGGAGCCUGUGAACC*GGGAGGCGCCGGUGAAAUACCACCCUG

Length

57 nucleotides

Bulged bases

5NDK|1|14|C|2136, 5NDK|1|14|G|2137, 5NDK|1|14|U|2138, 5NDK|1|14|A|2139, 5NDK|1|14|G|2150, 5NDK|1|14|A|2151, 5NDK|1|14|G|2156, 5NDK|1|14|U|2157, 5NDK|1|14|U|2192

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|14|C|2133
5NDK|1|14|U|2134
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|U|2147
5NDK|1|14|G|2148
5NDK|1|14|G|2149
5NDK|1|14|G|2150
5NDK|1|14|A|2151
5NDK|1|14|G|2152
5NDK|1|14|C|2153
5NDK|1|14|C|2154
5NDK|1|14|U|2155
5NDK|1|14|G|2156
5NDK|1|14|U|2157
5NDK|1|14|G|2158
5NDK|1|14|A|2159
5NDK|1|14|A|2160
5NDK|1|14|C|2161
5NDK|1|14|C|2162
*
5NDK|1|14|G|2180
5NDK|1|14|G|2181
5NDK|1|14|G|2182
5NDK|1|14|A|2183
5NDK|1|14|G|2184
5NDK|1|14|G|2185
5NDK|1|14|C|2186
5NDK|1|14|G|2187
5NDK|1|14|C|2188
5NDK|1|14|C|2189
5NDK|1|14|G|2190
5NDK|1|14|G|2191
5NDK|1|14|U|2192
5NDK|1|14|G|2193
5NDK|1|14|A|2194
5NDK|1|14|A|2195
5NDK|1|14|A|2196
5NDK|1|14|U|2197
5NDK|1|14|A|2198
5NDK|1|14|C|2199
5NDK|1|14|C|2200
5NDK|1|14|A|2201
5NDK|1|14|C|2202
5NDK|1|14|C|2203
5NDK|1|14|C|2204
5NDK|1|14|U|2205
5NDK|1|14|G|2206

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 13

Small subunit ribosomal RNA; SSU rRNA

Chain V4

Transfer RNA; tRNA