IL_1VY6_237

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

GGC*GUAC

Length

7 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_237 not in the Motif Atlas

Geometric match to IL_5FJC_003

Geometric discrepancy: 0.3153

The information below is about IL_5FJC_003

Detailed Annotation

Major groove platform with extra pair

Broad Annotation

Major groove platform

Motif group

IL_15698.5

Basepair signature

cWW-L-R-L-cWW

Number of instances in this motif group

11

Unit IDs

1VY6|1|DA|G|272|||D
1VY6|1|DA|G|272|||E
1VY6|1|DA|C|272|||F
*
1VY6|1|DA|G|363|||D
1VY6|1|DA|U|363|||E
1VY6|1|DA|A|363|||F
1VY6|1|DA|C|364

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain DI

50S ribosomal protein L9