J5_1VY5_012

3D structure

PDB id

1VY5 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.55 Å

Loop

Sequence

CGAUGAAG*CGAAUG*CG*CAC*GGG

Length

22 nucleotides

Bulged bases

1VY5|1|DA|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_1VY5_012 not in the Motif Atlas

Homologous match to J5_9DFE_001

Geometric discrepancy: 0.0568

The information below is about J5_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_01737.2

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

1VY5|1|DA|C|47
1VY5|1|DA|G|48
1VY5|1|DA|A|49
1VY5|1|DA|U|50
1VY5|1|DA|G|51
1VY5|1|DA|A|52
1VY5|1|DA|A|53
1VY5|1|DA|G|54
*
1VY5|1|DA|C|116
1VY5|1|DA|G|117
1VY5|1|DA|A|118
1VY5|1|DA|A|119
1VY5|1|DA|U|120
1VY5|1|DA|G|121
*
1VY5|1|DA|C|130
1VY5|1|DA|G|131
*
1VY5|1|DA|C|148
1VY5|1|DA|A|149
1VY5|1|DA|C|150
*
1VY5|1|DA|G|176
1VY5|1|DA|G|177
1VY5|1|DA|G|178

Current chains

Chain DA

23S Ribosomal RNA

Nearby chains

Chain D7

50S ribosomal protein L34

Chain DX

50S ribosomal protein L23