J4_5DOY_034

3D structure

PDB id

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

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with antibiotic Hygromycin A, mRNA and three tRNAs in the A, P and E sites at 2.6A 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

5DOY|1|2w|4SU|8, 5DOY|1|2w|U|47, 5DOY|1|2w|C|48

QA status

Unknown status

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_5DOY_034 not in the Motif Atlas

Homologous match to J4_3WQY_001

Geometric discrepancy: 0.2333

The information below is about J4_3WQY_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_95067.1

Basepair signature

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

Number of instances in this motif group

48

Unit IDs

5DOY|1|2w|A|7
5DOY|1|2w|4SU|8
5DOY|1|2w|A|9
5DOY|1|2w|G|10
*
5DOY|1|2w|C|25
5DOY|1|2w|A|26
5DOY|1|2w|G|27
*
5DOY|1|2w|C|43
5DOY|1|2w|G|44
5DOY|1|2w|U|45
5DOY|1|2w|7MG|46
5DOY|1|2w|U|47
5DOY|1|2w|C|48
5DOY|1|2w|C|49
*
5DOY|1|2w|G|65
5DOY|1|2w|U|66

Current chains

Chain 2w

A-site and E-site tRNAs

Nearby chains

Chain 2A

Large subunit ribosomal RNA; LSU rRNA