IL_1VY6_257

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

GCACU*AAAC

Length

9 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

IL_1VY6_257 not in the Motif Atlas

Homologous match to IL_7RQB_029

Geometric discrepancy: 0.1143

The information below is about IL_7RQB_029

Detailed Annotation

C-loop

Broad Annotation

No text annotation

Motif group

IL_02509.1

Basepair signature

cWW-tSW-cWS-cSH-tWH-R-R-cWW

Number of instances in this motif group

5

Unit IDs

1VY6|1|DA|G|864
1VY6|1|DA|C|865
1VY6|1|DA|A|866
1VY6|1|DA|C|867
1VY6|1|DA|U|868
*
1VY6|1|DA|A|909
1VY6|1|DA|A|910
1VY6|1|DA|A|911
1VY6|1|DA|C|912

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain DB

5S ribosomal RNA; 5S rRNA

Chain DQ

50S ribosomal protein L16

Chain DZ

50S ribosomal protein L25