IL_1VY6_301

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

CGAAAUUCCUUG*CCUG

Length

16 nucleotides

Bulged bases

1VY6|1|DA|A|1938, 1VY6|1|DA|U|1944, 1VY6|1|DA|U|1963

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_301 not in the Motif Atlas

Geometric match to IL_4WF9_077

Geometric discrepancy: 0.1457

The information below is about IL_4WF9_077

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_84014.1

Basepair signature

cWW-L-R-cHW-cWW-L-L-tSW-L

Number of instances in this motif group

8

Unit IDs

1VY6|1|DA|C|1934
1VY6|1|DA|G|1935
1VY6|1|DA|A|1936
1VY6|1|DA|A|1937
1VY6|1|DA|A|1938
1VY6|1|DA|U|1939
1VY6|1|DA|U|1940
1VY6|1|DA|C|1941
1VY6|1|DA|C|1942
1VY6|1|DA|U|1943
1VY6|1|DA|U|1944
1VY6|1|DA|G|1945
*
1VY6|1|DA|C|1961
1VY6|1|DA|C|1962
1VY6|1|DA|U|1963
1VY6|1|DA|G|1964

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain CA

Small subunit ribosomal RNA; SSU rRNA

Chain DD

50S ribosomal protein L2