J4_6ND5_014

3D structure

PDB id

6ND5 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with chloramphenicol and bound to mRNA and A-, P-, and E-site tRNAs at 2.60A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

A(4SU)AG*CAG*CGU(7MG)UCC*GU

Length

16 nucleotides

Bulged bases

6ND5|1|1w|4SU|8, 6ND5|1|1w|U|47, 6ND5|1|1w|C|48

QA status

Modified nucleotides: 4SU, 7MG

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_6ND5_014 not in the Motif Atlas

Homologous match to J4_3TUP_001

Geometric discrepancy: 0.294

The information below is about J4_3TUP_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_70449.28

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

55

Unit IDs

6ND5|1|1w|A|7
6ND5|1|1w|4SU|8
6ND5|1|1w|A|9
6ND5|1|1w|G|10
*
6ND5|1|1w|C|25
6ND5|1|1w|A|26
6ND5|1|1w|G|27
*
6ND5|1|1w|C|43
6ND5|1|1w|G|44
6ND5|1|1w|U|45
6ND5|1|1w|7MG|46
6ND5|1|1w|U|47
6ND5|1|1w|C|48
6ND5|1|1w|C|49
*
6ND5|1|1w|G|65
6ND5|1|1w|U|66

Current chains

Chain 1w

A-site and E-site tRNAs

Nearby chains

Chain 1A

Large subunit ribosomal RNA; LSU rRNA