IL_5NDK_076

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

GAAC*GAGUGAAAUAGAGC

Length

18 nucleotides

Bulged bases

5NDK|1|14|U|531, 5NDK|1|14|G|535

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_076 not in the Motif Atlas

Homologous match to IL_7RQB_014

Geometric discrepancy: 0.0572

The information below is about IL_7RQB_014

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_60992.6

Basepair signature

cWW-cWS-tSH-L-tHH-tWH-cWW-tSS-tSH-L-L

Number of instances in this motif group

6

Unit IDs

5NDK|1|14|G|509
5NDK|1|14|A|510
5NDK|1|14|A|511
5NDK|1|14|C|512
*
5NDK|1|14|G|523
5NDK|1|14|A|524
5NDK|1|14|G|525
5NDK|1|14|U|526
5NDK|1|14|G|527
5NDK|1|14|A|528
5NDK|1|14|A|529
5NDK|1|14|A|530
5NDK|1|14|U|531
5NDK|1|14|A|532
5NDK|1|14|G|533
5NDK|1|14|A|534
5NDK|1|14|G|535
5NDK|1|14|C|536

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain A5

50S ribosomal protein L22

Chain C5

50S ribosomal protein L24