IL_5VP2_072

3D structure

PDB id

5VP2 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

UCAAG*CGAAG

Length

10 nucleotides

Bulged bases

None detected

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

IL_5VP2_072 not in the Motif Atlas

Homologous match to IL_9DFE_074

Geometric discrepancy: 0.117

The information below is about IL_9DFE_074

Detailed Annotation

UAA/GAN with extra stack

Broad Annotation

UAA/GAN with extra stack

Motif group

IL_89021.4

Basepair signature

cWW-L-R-L-R-tHS-cWW

Number of instances in this motif group

8

Unit IDs

5VP2|1|1A|U|1882
5VP2|1|1A|C|1883
5VP2|1|1A|A|1884
5VP2|1|1A|A|1885
5VP2|1|1A|G|1886
*
5VP2|1|1A|C|1909
5VP2|1|1A|G|1910
5VP2|1|1A|A|1911
5VP2|1|1A|A|1912
5VP2|1|1A|G|1913

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1y

Transfer RNA; tRNA