J3_1VY7_058

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

1VY7|1|BA|U|504, 1VY7|1|BA|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_1VY7_058 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0409

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

1VY7|1|BA|G|30
1VY7|1|BA|C|31
*
1VY7|1|BA|G|474
1VY7|1|BA|U|475
1VY7|1|BA|G|476
1VY7|1|BA|A|477
1VY7|1|BA|A|478
1VY7|1|BA|A|479
1VY7|1|BA|A|480
1VY7|1|BA|G|481
1VY7|1|BA|A|482
1VY7|1|BA|A|483
1VY7|1|BA|C|484
*
1VY7|1|BA|G|496
1VY7|1|BA|A|497
1VY7|1|BA|G|498
1VY7|1|BA|U|499
1VY7|1|BA|G|500
1VY7|1|BA|A|501
1VY7|1|BA|A|502
1VY7|1|BA|A|503
1VY7|1|BA|U|504
1VY7|1|BA|A|505
1VY7|1|BA|G|506
1VY7|1|BA|A|507
1VY7|1|BA|G|508
1VY7|1|BA|C|509
1VY7|1|BA|C|510

Current chains

Chain BA

23S Ribosomal RNA

Nearby chains

Chain BU

50S ribosomal protein L20

Chain BW

50S ribosomal protein L22

Chain BY

50S ribosomal protein L24