IL_5NDK_305

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

GGGAG*CGAAC

Length

10 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_305 not in the Motif Atlas

Homologous match to IL_7RQB_075

Geometric discrepancy: 0.0859

The information below is about IL_7RQB_075

Detailed Annotation

Triple sheared

Broad Annotation

No text annotation

Motif group

IL_56467.8

Basepair signature

cWW-tSH-tSH-tHS-cWW

Number of instances in this motif group

29

Unit IDs

5NDK|1|1H|G|1890
5NDK|1|1H|G|1891
5NDK|1|1H|G|1892
5NDK|1|1H|A|1893
5NDK|1|1H|G|1894
*
5NDK|1|1H|C|1907
5NDK|1|1H|G|1908
5NDK|1|1H|A|1909
5NDK|1|1H|A|1910
5NDK|1|1H|C|1911

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain J8

50S ribosomal protein L28

Chain V1

Transfer RNA; tRNA