IL_1VY6_125

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

UGCGAAC*GGAGGUAUA

Length

16 nucleotides

Bulged bases

1VY6|1|BA|G|1801, 1VY6|1|BA|G|1816, 1VY6|1|BA|U|1820

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_125 not in the Motif Atlas

Homologous match to IL_7RQB_070

Geometric discrepancy: 0.0425

The information below is about IL_7RQB_070

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_17069.3

Basepair signature

cWW-tSH-tHH-cSS-tWW-tHH-tSS-cWW

Number of instances in this motif group

5

Unit IDs

1VY6|1|BA|U|1798
1VY6|1|BA|G|1799
1VY6|1|BA|C|1800
1VY6|1|BA|G|1801
1VY6|1|BA|A|1802
1VY6|1|BA|A|1803
1VY6|1|BA|C|1804
*
1VY6|1|BA|G|1813
1VY6|1|BA|G|1814
1VY6|1|BA|A|1815
1VY6|1|BA|G|1816
1VY6|1|BA|G|1817
1VY6|1|BA|U|1818
1VY6|1|BA|A|1819
1VY6|1|BA|U|1820
1VY6|1|BA|A|1821

Current chains

Chain BA

23S Ribosomal RNA

Nearby chains

Chain AA

Small subunit ribosomal RNA; SSU rRNA

Chain BD

50S ribosomal protein L2