J5_5NDJ_012

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

CGAUGAAG*CGAAUG*CG*CAC*GGG

Length

22 nucleotides

Bulged bases

5NDJ|1|1H|U|49

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

J5_5NDJ_012 not in the Motif Atlas

Homologous match to J5_9DFE_001

Geometric discrepancy: 0.0566

The information below is about J5_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_01737.2

Basepair signature

cWW-F-cWW-F-cWW-tSH-tHH-tHS-cWW-cWW-cWW-F

Number of instances in this motif group

5

Unit IDs

5NDJ|1|1H|C|46
5NDJ|1|1H|G|47
5NDJ|1|1H|A|48
5NDJ|1|1H|U|49
5NDJ|1|1H|G|50
5NDJ|1|1H|A|51
5NDJ|1|1H|A|52
5NDJ|1|1H|G|53
*
5NDJ|1|1H|C|114
5NDJ|1|1H|G|115
5NDJ|1|1H|A|116
5NDJ|1|1H|A|117
5NDJ|1|1H|U|118
5NDJ|1|1H|G|119
*
5NDJ|1|1H|C|128
5NDJ|1|1H|G|129
*
5NDJ|1|1H|C|148
5NDJ|1|1H|A|149
5NDJ|1|1H|C|150
*
5NDJ|1|1H|G|166
5NDJ|1|1H|G|167
5NDJ|1|1H|G|168

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain F8

50S ribosomal protein L23

Chain P8

50S ribosomal protein L34