J3_1VY6_029

3D structure

PDB id

1VY6 (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 short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.9 Å

Loop

Sequence

UG*CGCCGAUGG*CAG

Length

14 nucleotides

Bulged bases

1VY6|1|CA|U|723

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

J3_1VY6_029 not in the Motif Atlas

Homologous match to J3_5J7L_003

Geometric discrepancy: 0.1331

The information below is about J3_5J7L_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_11934.4

Basepair signature

cWW-cWW-tWW-cWW-F-F-F-F-F

Number of instances in this motif group

4

Unit IDs

1VY6|1|CA|U|672
1VY6|1|CA|G|673
*
1VY6|1|CA|C|717
1VY6|1|CA|G|718
1VY6|1|CA|C|719
1VY6|1|CA|C|720
1VY6|1|CA|G|721
1VY6|1|CA|A|722
1VY6|1|CA|U|723
1VY6|1|CA|G|724
1VY6|1|CA|G|725
*
1VY6|1|CA|C|732
1VY6|1|CA|A|733
1VY6|1|CA|G|734

Current chains

Chain CA

16S Ribosomal RNA

Nearby chains

Chain CF

30S ribosomal protein S6

Chain CK

30S ribosomal protein S11

Chain CO

30S ribosomal protein S15

Chain CR

30S ribosomal protein S18

Chain DD

50S ribosomal protein L2