J4_5J4B_014

3D structure

PDB id

5J4B (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with cisplatin (co-crystallized) and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

GGA(4SU)AG*CAG*CGU(7MG)UCC*GUCC

Length

20 nucleotides

Bulged bases

5J4B|1|1w|4SU|8, 5J4B|1|1w|U|47, 5J4B|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_5J4B_014 not in the Motif Atlas

Homologous match to J4_6GSK_031

Geometric discrepancy: 0.4498

The information below is about J4_6GSK_031

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_13620.1

Basepair signature

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

Number of instances in this motif group

1

Unit IDs

5J4B|1|1w|G|5
5J4B|1|1w|G|6
5J4B|1|1w|A|7
5J4B|1|1w|4SU|8
5J4B|1|1w|A|9
5J4B|1|1w|G|10
*
5J4B|1|1w|C|25
5J4B|1|1w|A|26
5J4B|1|1w|G|27
*
5J4B|1|1w|C|43
5J4B|1|1w|G|44
5J4B|1|1w|U|45
5J4B|1|1w|7MG|46
5J4B|1|1w|U|47
5J4B|1|1w|C|48
5J4B|1|1w|C|49
*
5J4B|1|1w|G|65
5J4B|1|1w|U|66
5J4B|1|1w|C|67
5J4B|1|1w|C|68

Current chains

Chain 1w

A-site and E-site tRNAs

Nearby chains

Chain 1A

Large subunit ribosomal RNA; LSU rRNA

Chain 1x

Transfer RNA; tRNA