J3_1VY6_068

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

1VY6|1|DA|U|504, 1VY6|1|DA|G|508

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

J3_1VY6_068 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0734

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.1

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

9

Unit IDs

1VY6|1|DA|G|30
1VY6|1|DA|C|31
*
1VY6|1|DA|G|474
1VY6|1|DA|U|475
1VY6|1|DA|G|476
1VY6|1|DA|A|477
1VY6|1|DA|A|478
1VY6|1|DA|A|479
1VY6|1|DA|A|480
1VY6|1|DA|G|481
1VY6|1|DA|A|482
1VY6|1|DA|A|483
1VY6|1|DA|C|484
*
1VY6|1|DA|G|496
1VY6|1|DA|A|497
1VY6|1|DA|G|498
1VY6|1|DA|U|499
1VY6|1|DA|G|500
1VY6|1|DA|A|501
1VY6|1|DA|A|502
1VY6|1|DA|A|503
1VY6|1|DA|U|504
1VY6|1|DA|A|505
1VY6|1|DA|G|506
1VY6|1|DA|A|507
1VY6|1|DA|G|508
1VY6|1|DA|C|509
1VY6|1|DA|C|510

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain DU

50S ribosomal protein L20

Chain DW

50S ribosomal protein L22

Chain DY

50S ribosomal protein L24