J4_1VY6_011

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

GACUG*CACAG*CGAC*GUAAC

Length

19 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

J4_1VY6_011 not in the Motif Atlas

Homologous match to J4_5J7L_025

Geometric discrepancy: 0.0558

The information below is about J4_5J7L_025

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_61477.5

Basepair signature

cWW-tSW-F-tHS-tHS-F-cWW-cWW-F-tHS-cWW

Number of instances in this motif group

4

Unit IDs

1VY6|1|BA|G|1772
1VY6|1|BA|A|1773
1VY6|1|BA|C|1774
1VY6|1|BA|U|1775
1VY6|1|BA|G|1776
*
1VY6|1|BA|C|1788
1VY6|1|BA|A|1789
1VY6|1|BA|C|1790
1VY6|1|BA|A|1791
1VY6|1|BA|G|1792
*
1VY6|1|BA|C|1827
1VY6|1|BA|G|1828
1VY6|1|BA|A|1829
1VY6|1|BA|C|1830
*
1VY6|1|BA|G|1975
1VY6|1|BA|U|1976
1VY6|1|BA|A|1977
1VY6|1|BA|A|1978
1VY6|1|BA|C|1979

Current chains

Chain BA

23S Ribosomal RNA

Nearby chains

Chain AA

Small subunit ribosomal RNA; SSU rRNA

Chain BD

50S ribosomal protein L2