IL_1VY6_037

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

GCA*UUCCC

Length

8 nucleotides

Bulged bases

1VY6|1|AA|C|934

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

IL_1VY6_037 not in the Motif Atlas

Homologous match to IL_5J7L_041

Geometric discrepancy: 0.1537

The information below is about IL_5J7L_041

Detailed Annotation

Minor groove platform

Broad Annotation

No text annotation

Motif group

IL_47078.3

Basepair signature

cWW-cWS-L-cWW-L

Number of instances in this motif group

4

Unit IDs

1VY6|1|AA|G|933
1VY6|1|AA|C|934
1VY6|1|AA|A|935
*
1VY6|1|AA|U|1380
1VY6|1|AA|U|1381
1VY6|1|AA|C|1382
1VY6|1|AA|C|1383
1VY6|1|AA|C|1384

Current chains

Chain AA

16S Ribosomal RNA

Nearby chains

Chain AG

30S ribosomal protein S7

Chain AI

30S ribosomal protein S9

Chain AX

Transfer RNA; tRNA