J5_1VY6_017

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

GCAAGUUGG*UG*CC*GUGAACAGG*CGC

Length

25 nucleotides

Bulged bases

1VY6|1|DA|G|1758, 1VY6|1|DA|G|1763

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

J5_1VY6_017 not in the Motif Atlas

Homologous match to J5_9DFE_005

Geometric discrepancy: 0.0696

The information below is about J5_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_99177.1

Basepair signature

cWW-F-F-F-cWW-F-F-F-F-F-F-F-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

10

Unit IDs

1VY6|1|DA|G|1674
1VY6|1|DA|C|1675
1VY6|1|DA|A|1676
1VY6|1|DA|A|1677
1VY6|1|DA|G|1678
1VY6|1|DA|U|1679
1VY6|1|DA|U|1680
1VY6|1|DA|G|1681
1VY6|1|DA|G|1682
*
1VY6|1|DA|U|1706
1VY6|1|DA|G|1707
*
1VY6|1|DA|C|1751
1VY6|1|DA|C|1752
*
1VY6|1|DA|G|1756
1VY6|1|DA|U|1757
1VY6|1|DA|G|1758
1VY6|1|DA|A|1759
1VY6|1|DA|A|1760
1VY6|1|DA|C|1761
1VY6|1|DA|A|1762
1VY6|1|DA|G|1763
1VY6|1|DA|G|1764
*
1VY6|1|DA|C|1988
1VY6|1|DA|G|1989
1VY6|1|DA|C|1990

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain CA

Small subunit ribosomal RNA; SSU rRNA

Chain DE

50S ribosomal protein L3

Chain DO

50S ribosomal protein L14

Chain DT

50S ribosomal protein L19