IL_5NDJ_303

3D structure

PDB id

5NDJ (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)

Experimental method

X-RAY DIFFRACTION

Resolution

3.15 Å

Loop

Sequence

CGAAAUUCCUUG*CCUG

Length

16 nucleotides

Bulged bases

5NDJ|1|1H|A|1963, 5NDJ|1|1H|U|1969

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_5NDJ_303 not in the Motif Atlas

Homologous match to IL_7A0S_072

Geometric discrepancy: 0.1559

The information below is about IL_7A0S_072

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_04332.3

Basepair signature

cWW-L-R-L-cWW-L-L-R-L-R-L

Number of instances in this motif group

2

Unit IDs

5NDJ|1|1H|C|1959
5NDJ|1|1H|G|1960
5NDJ|1|1H|A|1961
5NDJ|1|1H|A|1962
5NDJ|1|1H|A|1963
5NDJ|1|1H|U|1964
5NDJ|1|1H|U|1965
5NDJ|1|1H|C|1966
5NDJ|1|1H|C|1967
5NDJ|1|1H|U|1968
5NDJ|1|1H|U|1969
5NDJ|1|1H|G|1970
*
5NDJ|1|1H|C|1986
5NDJ|1|1H|C|1987
5NDJ|1|1H|U|1988
5NDJ|1|1H|G|1989

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L2

Chain 13

Small subunit ribosomal RNA; SSU rRNA

Chain W1

Transfer RNA; tRNA