J3_1VY7_049

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

GCC*GCCUAGUGAACC*GAUCAAC

Length

22 nucleotides

Bulged bases

1VY7|1|DA|A|2426

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_049 not in the Motif Atlas

Homologous match to J3_9DFE_015

Geometric discrepancy: 0.0636

The information below is about J3_9DFE_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_04772.1

Basepair signature

cWW-F-tHH-cWW-tHW-tHW-F-cWW-F-F-F-F-F

Number of instances in this motif group

8

Unit IDs

1VY7|1|DA|G|2282
1VY7|1|DA|C|2283
1VY7|1|DA|C|2284
*
1VY7|1|DA|G|2384
1VY7|1|DA|C|2385
1VY7|1|DA|C|2386
1VY7|1|DA|U|2387
1VY7|1|DA|A|2388
1VY7|1|DA|G|2389
1VY7|1|DA|U|2390
1VY7|1|DA|G|2391
1VY7|1|DA|A|2392
1VY7|1|DA|A|2393
1VY7|1|DA|C|2394
1VY7|1|DA|C|2395
*
1VY7|1|DA|G|2421
1VY7|1|DA|A|2422
1VY7|1|DA|U|2423
1VY7|1|DA|C|2424
1VY7|1|DA|A|2425
1VY7|1|DA|A|2426
1VY7|1|DA|C|2427

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain CY

Transfer RNA; tRNA

Chain D0

50S ribosomal protein L27

Chain D1

50S ribosomal protein L28

Chain D6

50S ribosomal protein L33

Chain D8

50S ribosomal protein L35

Chain DP

50S ribosomal protein L15