J4_1VY4_020

3D structure

PDB id

1VY4 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing acylated tRNA-substrates in the A and P sites.

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

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

Length

16 nucleotides

Bulged bases

1VY4|1|CW|4SU|8, 1VY4|1|CW|U|47, 1VY4|1|CW|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_1VY4_020 not in the Motif Atlas

Homologous match to J4_6UGG_002

Geometric discrepancy: 0.2818

The information below is about J4_6UGG_002

Detailed Annotation

No text annotation

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

1VY4|1|CW|A|7
1VY4|1|CW|4SU|8
1VY4|1|CW|A|9
1VY4|1|CW|G|10
*
1VY4|1|CW|C|25
1VY4|1|CW|A|26
1VY4|1|CW|G|27
*
1VY4|1|CW|C|43
1VY4|1|CW|G|44
1VY4|1|CW|U|45
1VY4|1|CW|7MG|46
1VY4|1|CW|U|47
1VY4|1|CW|C|48
1VY4|1|CW|C|49
*
1VY4|1|CW|G|65
1VY4|1|CW|U|66

Current chains

Chain CW

A-site tRNA

Nearby chains

Chain DA

Large subunit ribosomal RNA; LSU rRNA