J3_1VY6_004

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

CUAG*CGAAG*CGUUAAG

Length

16 nucleotides

Bulged bases

1VY6|1|AA|U|871

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_1VY6_004 not in the Motif Atlas

Homologous match to J3_4LFB_001

Geometric discrepancy: 0.0827

The information below is about J3_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_02285.1

Basepair signature

cWW-tWW-tHS-F-cWW-tHS-cWW-F

Number of instances in this motif group

2

Unit IDs

1VY6|1|AA|C|826
1VY6|1|AA|U|827
1VY6|1|AA|A|828
1VY6|1|AA|G|829
*
1VY6|1|AA|C|857
1VY6|1|AA|G|858
1VY6|1|AA|A|859
1VY6|1|AA|A|860
1VY6|1|AA|G|861
*
1VY6|1|AA|C|868
1VY6|1|AA|G|869
1VY6|1|AA|U|870
1VY6|1|AA|U|871
1VY6|1|AA|A|872
1VY6|1|AA|A|873
1VY6|1|AA|G|874

Current chains

Chain AA

16S Ribosomal RNA

Nearby chains

Chain AB

30S ribosomal protein S2

Chain AH

30S ribosomal protein S8