J5_1VY6_019

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

UUUA*UUUG*CG*CG*CGGAUAAAA

Length

21 nucleotides

Bulged bases

1VY6|1|DA|U|2076, 1VY6|1|DA|G|2428, 1VY6|1|DA|G|2429, 1VY6|1|DA|A|2430, 1VY6|1|DA|U|2431

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

J5_1VY6_019 not in the Motif Atlas

Homologous match to J5_9DFE_007

Geometric discrepancy: 0.0561

The information below is about J5_9DFE_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_39529.2

Basepair signature

cWW-cWH-cWH-F-cWW-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

4

Unit IDs

1VY6|1|DA|U|2074
1VY6|1|DA|U|2075
1VY6|1|DA|U|2076
1VY6|1|DA|A|2077
*
1VY6|1|DA|U|2243
1VY6|1|DA|U|2244
1VY6|1|DA|U|2245
1VY6|1|DA|G|2246
*
1VY6|1|DA|C|2258
1VY6|1|DA|G|2259
*
1VY6|1|DA|C|2281
1VY6|1|DA|G|2282
*
1VY6|1|DA|C|2427
1VY6|1|DA|G|2428
1VY6|1|DA|G|2429
1VY6|1|DA|A|2430
1VY6|1|DA|U|2431
1VY6|1|DA|A|2432
1VY6|1|DA|A|2433
1VY6|1|DA|A|2434
1VY6|1|DA|A|2435

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain D0

50S ribosomal protein L27

Chain D1

50S ribosomal protein L28

Chain D6

50S ribosomal protein L33

Chain DD

50S ribosomal protein L2

Chain DP

50S ribosomal protein L15