J3_1VY6_069

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

CUCG*CGAUAGCGCACCAGUAC*GGAAAG

Length

27 nucleotides

Bulged bases

1VY6|1|DA|U|448, 1VY6|1|DA|C|456

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_069 not in the Motif Atlas

Homologous match to J3_9DFE_003

Geometric discrepancy: 0.0854

The information below is about J3_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_07616.1

Basepair signature

cWW-cSS-tSS-tSW-tHW-cWW-tWH-F-F-tHH-tSS-tWH-F-tHS-cWW-F-cSH

Number of instances in this motif group

10

Unit IDs

1VY6|1|DA|C|32
1VY6|1|DA|U|33
1VY6|1|DA|C|34
1VY6|1|DA|G|35
*
1VY6|1|DA|C|445
1VY6|1|DA|G|446
1VY6|1|DA|A|447
1VY6|1|DA|U|448
1VY6|1|DA|A|449
1VY6|1|DA|G|450
1VY6|1|DA|C|451
1VY6|1|DA|G|452
1VY6|1|DA|C|453
1VY6|1|DA|A|454
1VY6|1|DA|C|455
1VY6|1|DA|C|456
1VY6|1|DA|A|457
1VY6|1|DA|G|458
1VY6|1|DA|U|459
1VY6|1|DA|A|460
1VY6|1|DA|C|461
*
1VY6|1|DA|G|468
1VY6|1|DA|G|469
1VY6|1|DA|A|470
1VY6|1|DA|A|471
1VY6|1|DA|A|472
1VY6|1|DA|G|473

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain D7

50S ribosomal protein L34

Chain DF

50S ribosomal protein L4

Chain DU

50S ribosomal protein L20

Chain DX

50S ribosomal protein L23