IL_5VP2_040

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

GAUG*CGC

Length

7 nucleotides

Bulged bases

5VP2|1|1A|U|1079

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_040 not in the Motif Atlas

Homologous match to IL_9DFE_040

Geometric discrepancy: 0.0687

The information below is about IL_9DFE_040

Detailed Annotation

Isolated non-canonical cWW pair

Broad Annotation

No text annotation

Motif group

IL_76400.1

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

15

Unit IDs

5VP2|1|1A|G|1077
5VP2|1|1A|A|1078
5VP2|1|1A|U|1079
5VP2|1|1A|G|1080
*
5VP2|1|1A|C|1167
5VP2|1|1A|G|1168
5VP2|1|1A|C|1169

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 19

50S ribosomal protein L36

Chain 1H

50S ribosomal protein L6

Chain 1Q

50S ribosomal protein L16