J4_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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

1VY6|1|DA|U|405

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

J4_1VY6_019 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.0731

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_45801.6

Basepair signature

cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-F-cWW

Number of instances in this motif group

7

Unit IDs

1VY6|1|DA|C|268
1VY6|1|DA|U|269
*
1VY6|1|DA|G|370
1VY6|1|DA|A|371
1VY6|1|DA|G|372
1VY6|1|DA|U|373
1VY6|1|DA|A|374
1VY6|1|DA|C|375
*
1VY6|1|DA|G|399
1VY6|1|DA|G|400
1VY6|1|DA|A|401
1VY6|1|DA|A|402
1VY6|1|DA|U|403
1VY6|1|DA|C|404
1VY6|1|DA|U|405
1VY6|1|DA|G|406
*
1VY6|1|DA|U|421
1VY6|1|DA|A|422
1VY6|1|DA|A|423
1VY6|1|DA|G|424

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain D1

50S ribosomal protein L28

Chain DI

50S ribosomal protein L9