J5_1VY6_001

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

CUGG*CUUG*CUGAAC*GGUAAUAG*CGAG

Length

26 nucleotides

Bulged bases

None detected

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_001 not in the Motif Atlas

Homologous match to J5_4LFB_001

Geometric discrepancy: 0.0709

The information below is about J5_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_70703.1

Basepair signature

cWW-F-tWH-F-F-cWW-cWW-cWH-cWH-cWW-tSH-tWH-tHW-tHS-cWW

Number of instances in this motif group

1

Unit IDs

1VY6|1|AA|C|36
1VY6|1|AA|U|37
1VY6|1|AA|G|38
1VY6|1|AA|G|39
*
1VY6|1|AA|C|403
1VY6|1|AA|U|404
1VY6|1|AA|U|405
1VY6|1|AA|G|406
*
1VY6|1|AA|C|436
1VY6|1|AA|U|437
1VY6|1|AA|G|438
1VY6|1|AA|A|439
1VY6|1|AA|A|441
1VY6|1|AA|C|442
*
1VY6|1|AA|G|492
1VY6|1|AA|G|493
1VY6|1|AA|U|494
1VY6|1|AA|A|495
1VY6|1|AA|A|496
1VY6|1|AA|U|498
1VY6|1|AA|A|499
1VY6|1|AA|G|500
*
1VY6|1|AA|C|545
1VY6|1|AA|G|546
1VY6|1|AA|A|547
1VY6|1|AA|G|548

Current chains

Chain AA

16S Ribosomal RNA

Nearby chains

Chain AD

30S ribosomal protein S4

Chain AL

30S ribosomal protein S12