J4_1VY7_023

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

UC*GGUUAG*CU*ACCCGUA

Length

17 nucleotides

Bulged bases

1VY7|1|DA|U|1341

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_1VY7_023 not in the Motif Atlas

Homologous match to J4_9DFE_005

Geometric discrepancy: 0.0653

The information below is about J4_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_48150.1

Basepair signature

cWW-cWW-tHW-F-F-F-F-F-F-cWW-cWW

Number of instances in this motif group

8

Unit IDs

1VY7|1|DA|U|1313
1VY7|1|DA|C|1314
*
1VY7|1|DA|G|1338
1VY7|1|DA|G|1339
1VY7|1|DA|U|1340
1VY7|1|DA|U|1341
1VY7|1|DA|A|1342
1VY7|1|DA|G|1343
*
1VY7|1|DA|C|1404
1VY7|1|DA|U|1405
*
1VY7|1|DA|A|1597
1VY7|1|DA|C|1598
1VY7|1|DA|C|1599
1VY7|1|DA|C|1600
1VY7|1|DA|G|1601
1VY7|1|DA|U|1602
1VY7|1|DA|A|1603

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain D7

50S ribosomal protein L34

Chain DX

50S ribosomal protein L23