IL_1VY6_295

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

CCGG*CG

Length

6 nucleotides

Bulged bases

1VY6|1|DA|C|1838

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_295 not in the Motif Atlas

Homologous match to IL_7RQB_071

Geometric discrepancy: 0.0954

The information below is about IL_7RQB_071

Detailed Annotation

Minor groove platform, major groove intercalation

Broad Annotation

Minor groove platform, major groove intercalation

Motif group

IL_88739.3

Basepair signature

cWW-L-cWW

Number of instances in this motif group

11

Unit IDs

1VY6|1|DA|C|1837
1VY6|1|DA|C|1838
1VY6|1|DA|G|1839
1VY6|1|DA|G|1840
*
1VY6|1|DA|C|1902
1VY6|1|DA|G|1903

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain CA

Small subunit ribosomal RNA; SSU rRNA

Chain DD

50S ribosomal protein L2