J3_5VP2_031

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

CGAGCUA*UAG*CGAG

Length

14 nucleotides

Bulged bases

5VP2|1|2A|G|686, 5VP2|1|2A|G|792, 5VP2|1|2A|A|793

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

J3_5VP2_031 not in the Motif Atlas

Homologous match to J3_9DFE_007

Geometric discrepancy: 0.07

The information below is about J3_9DFE_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_46658.1

Basepair signature

cWW-tWH-cWW-tSW-F-F-cWW

Number of instances in this motif group

10

Unit IDs

5VP2|1|2A|C|683
5VP2|1|2A|G|684
5VP2|1|2A|A|685
5VP2|1|2A|G|686
5VP2|1|2A|C|687
5VP2|1|2A|U|688
5VP2|1|2A|A|689
*
5VP2|1|2A|U|773
5VP2|1|2A|A|774
5VP2|1|2A|G|775
*
5VP2|1|2A|C|791
5VP2|1|2A|G|792
5VP2|1|2A|A|793
5VP2|1|2A|G|794

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 27

50S ribosomal protein L34

Chain 2D

50S ribosomal protein L2