J3_1VY6_031

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

CAAG*CUAGUAA*UGAAUACG

Length

19 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

J3_1VY6_031 not in the Motif Atlas

Homologous match to J3_4LFB_002

Geometric discrepancy: 0.1035

The information below is about J3_4LFB_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_85722.1

Basepair signature

cWW-F-F-cSS-F-cWW-tHH-tWW-F-tWH-tHS-cSH-cWW

Number of instances in this motif group

5

Unit IDs

1VY6|1|CA|C|936
1VY6|1|CA|A|937
1VY6|1|CA|A|938
1VY6|1|CA|G|939
*
1VY6|1|CA|C|1344
1VY6|1|CA|U|1345
1VY6|1|CA|A|1346
1VY6|1|CA|G|1347
1VY6|1|CA|U|1348
1VY6|1|CA|A|1349
1VY6|1|CA|A|1350
*
1VY6|1|CA|U|1372
1VY6|1|CA|G|1373
1VY6|1|CA|A|1374
1VY6|1|CA|A|1375
1VY6|1|CA|U|1376
1VY6|1|CA|A|1377
1VY6|1|CA|C|1378
1VY6|1|CA|G|1379

Current chains

Chain CA

16S Ribosomal RNA

Nearby chains

Chain CG

30S ribosomal protein S7

Chain CI

30S ribosomal protein S9