IL_1VY6_187

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

GGACG*CGGUAC

Length

11 nucleotides

Bulged bases

None detected

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

IL_1VY6_187 not in the Motif Atlas

Geometric match to IL_4LFB_018

Geometric discrepancy: 0.1557

The information below is about IL_4LFB_018

Detailed Annotation

6x5 Sarcin-Ricin; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_82100.1

Basepair signature

cWW-tWW-cSH-tWH-tHS-cWW

Number of instances in this motif group

3

Unit IDs

1VY6|1|CA|G|446
1VY6|1|CA|G|447
1VY6|1|CA|A|448
1VY6|1|CA|C|449
1VY6|1|CA|G|450
*
1VY6|1|CA|C|483
1VY6|1|CA|G|484
1VY6|1|CA|G|485
1VY6|1|CA|U|486
1VY6|1|CA|A|487
1VY6|1|CA|C|488

Current chains

Chain CA

16S Ribosomal RNA

Nearby chains

Chain CD

30S ribosomal protein S4

Chain CP

30S ribosomal protein S16