IL_5NDJ_056

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

GUC*GUC

Length

6 nucleotides

Bulged bases

None detected

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_056 not in the Motif Atlas

Geometric match to IL_3GM7_005

Geometric discrepancy: 0.1253

The information below is about IL_3GM7_005

Detailed Annotation

Isolated non-canonical cWW pair

Broad Annotation

No text annotation

Motif group

IL_87907.2

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

179

Unit IDs

5NDJ|1|13|G|2033
5NDJ|1|13|U|2034
5NDJ|1|13|C|2035
*
5NDJ|1|13|G|2117
5NDJ|1|13|U|2118
5NDJ|1|13|C|2119

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 1H

Large subunit ribosomal RNA; LSU rRNA

Chain 3I

30S ribosomal protein S12

Chain W1

Transfer RNA; tRNA

Chain Y1

mRNA