J3_5VP2_008

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

CAAG*CGCAAAC*GUG

Length

14 nucleotides

Bulged bases

5VP2|1|1A|A|1655

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_008 not in the Motif Atlas

Homologous match to J3_9DFE_011

Geometric discrepancy: 0.0709

The information below is about J3_9DFE_011

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_47341.1

Basepair signature

cWW-tHH-F-tHW-tHS-tWW-cWW-cWW-F

Number of instances in this motif group

4

Unit IDs

5VP2|1|1A|C|1352
5VP2|1|1A|A|1353
5VP2|1|1A|A|1354
5VP2|1|1A|G|1355
*
5VP2|1|1A|C|1651
5VP2|1|1A|G|1652
5VP2|1|1A|C|1653
5VP2|1|1A|A|1654
5VP2|1|1A|A|1655
5VP2|1|1A|A|1656
5VP2|1|1A|C|1657
*
5VP2|1|1A|G|1666
5VP2|1|1A|U|1667
5VP2|1|1A|G|1668

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 17

50S ribosomal protein L34