J4_1VY6_026

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

UUG*CG*CCUAAGGUAG*CGAAAA

Length

21 nucleotides

Bulged bases

1VY6|1|DA|A|1971

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_026 not in the Motif Atlas

Homologous match to J4_9DFE_008

Geometric discrepancy: 0.0785

The information below is about J4_9DFE_008

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_42306.1

Basepair signature

cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tWW-F-cSH-F-F

Number of instances in this motif group

5

Unit IDs

1VY6|1|DA|U|1833
1VY6|1|DA|U|1834
1VY6|1|DA|G|1835
*
1VY6|1|DA|C|1905
1VY6|1|DA|G|1906
*
1VY6|1|DA|C|1924
1VY6|1|DA|C|1925
1VY6|1|DA|U|1926
1VY6|1|DA|A|1927
1VY6|1|DA|A|1928
1VY6|1|DA|G|1929
1VY6|1|DA|G|1930
1VY6|1|DA|U|1931
1VY6|1|DA|A|1932
1VY6|1|DA|G|1933
*
1VY6|1|DA|C|1967
1VY6|1|DA|G|1968
1VY6|1|DA|A|1969
1VY6|1|DA|A|1970
1VY6|1|DA|A|1971
1VY6|1|DA|A|1972

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain CA

Small subunit ribosomal RNA; SSU rRNA

Chain CX

Transfer RNA; tRNA

Chain DD

50S ribosomal protein L2