J5_1VY7_017

3D structure

PDB id

1VY7 (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-Cytidine-Puromycin in the A site and acylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

GCAAGUUGG*UG*CC*GUGAACAGG*CGC

Length

25 nucleotides

Bulged bases

1VY7|1|DA|G|1758, 1VY7|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_1VY7_017 not in the Motif Atlas

Homologous match to J5_9DFE_005

Geometric discrepancy: 0.0536

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

1VY7|1|DA|G|1674
1VY7|1|DA|C|1675
1VY7|1|DA|A|1676
1VY7|1|DA|A|1677
1VY7|1|DA|G|1678
1VY7|1|DA|U|1679
1VY7|1|DA|U|1680
1VY7|1|DA|G|1681
1VY7|1|DA|G|1682
*
1VY7|1|DA|U|1706
1VY7|1|DA|G|1707
*
1VY7|1|DA|C|1751
1VY7|1|DA|C|1752
*
1VY7|1|DA|G|1756
1VY7|1|DA|U|1757
1VY7|1|DA|G|1758
1VY7|1|DA|A|1759
1VY7|1|DA|A|1760
1VY7|1|DA|C|1761
1VY7|1|DA|A|1762
1VY7|1|DA|G|1763
1VY7|1|DA|G|1764
*
1VY7|1|DA|C|1988
1VY7|1|DA|G|1989
1VY7|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