J5_1VY6_003

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

CGAUGAAG*CGAAUG*CG*CAC*GGG

Length

22 nucleotides

Bulged bases

1VY6|1|BA|U|50

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_003 not in the Motif Atlas

Homologous match to J5_9DFE_001

Geometric discrepancy: 0.0503

The information below is about J5_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_27223.1

Basepair signature

cWW-cWW-cWW-cWW-F-cWW-F-tSH-F-tHH-tHS-cWW

Number of instances in this motif group

7

Unit IDs

1VY6|1|BA|C|47
1VY6|1|BA|G|48
1VY6|1|BA|A|49
1VY6|1|BA|U|50
1VY6|1|BA|G|51
1VY6|1|BA|A|52
1VY6|1|BA|A|53
1VY6|1|BA|G|54
*
1VY6|1|BA|C|116
1VY6|1|BA|G|117
1VY6|1|BA|A|118
1VY6|1|BA|A|119
1VY6|1|BA|U|120
1VY6|1|BA|G|121
*
1VY6|1|BA|C|130
1VY6|1|BA|G|131
*
1VY6|1|BA|C|148
1VY6|1|BA|A|149
1VY6|1|BA|C|150
*
1VY6|1|BA|G|176
1VY6|1|BA|G|177
1VY6|1|BA|G|178

Current chains

Chain BA

23S Ribosomal RNA

Nearby chains

Chain B7

50S ribosomal protein L34

Chain BX

50S ribosomal protein L23