J4_5NDJ_014

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

GGGC*GAC*GGAAG*CGC

Length

15 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_014 not in the Motif Atlas

Homologous match to J4_9DFE_010

Geometric discrepancy: 0.0832

The information below is about J4_9DFE_010

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_77044.4

Basepair signature

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

Number of instances in this motif group

3

Unit IDs

5NDJ|1|14|G|2658
5NDJ|1|14|G|2659
5NDJ|1|14|G|2660
5NDJ|1|14|C|2661
*
5NDJ|1|14|G|2689
5NDJ|1|14|A|2690
5NDJ|1|14|C|2691
*
5NDJ|1|14|G|2747
5NDJ|1|14|G|2748
5NDJ|1|14|A|2749
5NDJ|1|14|A|2750
5NDJ|1|14|G|2751
*
5NDJ|1|14|C|2785
5NDJ|1|14|G|2786
5NDJ|1|14|C|2787

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 15

50S ribosomal protein L13

Chain 25

50S ribosomal protein L14

Chain 29

50S ribosomal protein L3