J4_5NDK_024

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

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_5NDK_024 not in the Motif Atlas

Homologous match to J4_9DFE_007

Geometric discrepancy: 0.0476

The information below is about J4_9DFE_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61477.6

Basepair signature

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

Number of instances in this motif group

4

Unit IDs

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

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L2

Chain 13

Small subunit ribosomal RNA; SSU rRNA