IL_5NDK_300

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

UGCGAAC*GGAGGUAUA

Length

16 nucleotides

Bulged bases

5NDK|1|1H|G|1835, 5NDK|1|1H|G|1850, 5NDK|1|1H|U|1854

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_300 not in the Motif Atlas

Homologous match to IL_7RQB_070

Geometric discrepancy: 0.0425

The information below is about IL_7RQB_070

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_17069.3

Basepair signature

cWW-tSH-tHH-cSS-tWW-tHH-tSS-cWW

Number of instances in this motif group

5

Unit IDs

5NDK|1|1H|U|1832
5NDK|1|1H|G|1833
5NDK|1|1H|C|1834
5NDK|1|1H|G|1835
5NDK|1|1H|A|1836
5NDK|1|1H|A|1837
5NDK|1|1H|C|1838
*
5NDK|1|1H|G|1847
5NDK|1|1H|G|1848
5NDK|1|1H|A|1849
5NDK|1|1H|G|1850
5NDK|1|1H|G|1851
5NDK|1|1H|U|1852
5NDK|1|1H|A|1853
5NDK|1|1H|U|1854
5NDK|1|1H|A|1855

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L2

Chain 13

Small subunit ribosomal RNA; SSU rRNA