J4_5NDJ_011

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

GACUG*CACAG*CGAC*GUAAC

Length

19 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

J4_5NDJ_011 not in the Motif Atlas

Homologous match to J4_5J7L_025

Geometric discrepancy: 0.0462

The information below is about J4_5J7L_025

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61477.5

Basepair signature

cWW-tSW-F-tHS-tHS-F-cWW-cWW-F-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5NDJ|1|14|G|1806
5NDJ|1|14|A|1807
5NDJ|1|14|C|1808
5NDJ|1|14|U|1809
5NDJ|1|14|G|1810
*
5NDJ|1|14|C|1822
5NDJ|1|14|A|1823
5NDJ|1|14|C|1824
5NDJ|1|14|A|1825
5NDJ|1|14|G|1826
*
5NDJ|1|14|C|1861
5NDJ|1|14|G|1862
5NDJ|1|14|A|1863
5NDJ|1|14|C|1864
*
5NDJ|1|14|G|2000
5NDJ|1|14|U|2001
5NDJ|1|14|A|2002
5NDJ|1|14|A|2003
5NDJ|1|14|C|2004

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L2

Chain 1G

Small subunit ribosomal RNA; SSU rRNA