IL_5NDK_357

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

UGA*UG

Length

5 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_5NDK_357 not in the Motif Atlas

Homologous match to IL_9DFE_093

Geometric discrepancy: 0.0962

The information below is about IL_9DFE_093

Detailed Annotation

Major groove platform

Broad Annotation

No text annotation

Motif group

IL_48076.8

Basepair signature

cWW-cSH-cWW

Number of instances in this motif group

43

Unit IDs

5NDK|1|14|U|2472
5NDK|1|14|G|2473
5NDK|1|14|A|2474
*
5NDK|1|14|U|2508
5NDK|1|14|G|2509

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 45

50S ribosomal protein L16

Chain E5

50S ribosomal protein L27

Chain W4

Transfer RNA; tRNA