IL_5NDK_027

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*UGAC

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_5NDK_027 not in the Motif Atlas

Geometric match to IL_4LFB_027

Geometric discrepancy: 0.0817

The information below is about IL_4LFB_027

Detailed Annotation

Major groove platform; stack outside cWW

Broad Annotation

Major groove platform

Motif group

IL_74641.2

Basepair signature

cWW-tSH-cWW-L

Number of instances in this motif group

33

Unit IDs

5NDK|1|13|G|1283
5NDK|1|13|A|1284
*
5NDK|1|13|U|1380
5NDK|1|13|G|1381
5NDK|1|13|A|1382
5NDK|1|13|C|1383

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 6I

30S ribosomal protein S15

Chain 7E

30S ribosomal protein S8