J3_1VY7_071

3D structure

PDB id

1VY7 (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-Cytidine-Puromycin in the A site and acylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

CGAAG*CGCCAGAGAG*CGUAG

Length

20 nucleotides

Bulged bases

1VY7|1|DA|G|321

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_1VY7_071 not in the Motif Atlas

Homologous match to J3_9DFE_006

Geometric discrepancy: 0.0628

The information below is about J3_9DFE_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_77124.1

Basepair signature

cWW-tSH-cHH-cSW-F-tHS-cWW-cWW-F-F-cWW-F

Number of instances in this motif group

4

Unit IDs

1VY7|1|DA|C|297
1VY7|1|DA|G|298
1VY7|1|DA|A|299
1VY7|1|DA|A|300
1VY7|1|DA|G|301
*
1VY7|1|DA|C|316
1VY7|1|DA|G|317
1VY7|1|DA|C|318
1VY7|1|DA|C|319
1VY7|1|DA|A|320
1VY7|1|DA|G|321
1VY7|1|DA|A|322
1VY7|1|DA|G|323
1VY7|1|DA|A|324
1VY7|1|DA|G|325
*
1VY7|1|DA|C|337
1VY7|1|DA|G|338
1VY7|1|DA|U|339
1VY7|1|DA|A|340
1VY7|1|DA|G|341

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain DF

50S ribosomal protein L4

Chain DY

50S ribosomal protein L24