IL_5NDK_158

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

UG*CAAG

Length

6 nucleotides

Bulged bases

5NDK|1|14|A|2557

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_158 not in the Motif Atlas

Homologous match to IL_7RQB_099

Geometric discrepancy: 0.0652

The information below is about IL_7RQB_099

Detailed Annotation

Major groove platform with intercalation

Broad Annotation

Major groove platform

Motif group

IL_95601.3

Basepair signature

cWW-tSH-cWW

Number of instances in this motif group

10

Unit IDs

5NDK|1|14|U|2537
5NDK|1|14|G|2538
*
5NDK|1|14|C|2555
5NDK|1|14|A|2556
5NDK|1|14|A|2557
5NDK|1|14|G|2558

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 15

50S ribosomal protein L13