IL_5NDK_139

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

GA*UACC

Length

6 nucleotides

Bulged bases

5NDK|1|14|A|2454

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_139 not in the Motif Atlas

Homologous match to IL_5J7L_324

Geometric discrepancy: 0.0822

The information below is about IL_5J7L_324

Detailed Annotation

Minor groove platform

Broad Annotation

No text annotation

Motif group

IL_51454.3

Basepair signature

cWW-cSH-cWW

Number of instances in this motif group

45

Unit IDs

5NDK|1|14|G|2095
5NDK|1|14|A|2096
*
5NDK|1|14|U|2453
5NDK|1|14|A|2454
5NDK|1|14|C|2455
5NDK|1|14|C|2456

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L2

Chain X4

Transfer RNA; tRNA