IL_5VP2_237

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

UGCGAAC*GGAGGUAUA

Length

16 nucleotides

Bulged bases

5VP2|1|2A|G|1801, 5VP2|1|2A|G|1816, 5VP2|1|2A|U|1820

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_237 not in the Motif Atlas

Homologous match to IL_9DFE_070

Geometric discrepancy: 0.0766

The information below is about IL_9DFE_070

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_17069.6

Basepair signature

cWW-tSH-tHH-cSS-tWW-tHH-tSS-cWW

Number of instances in this motif group

5

Unit IDs

5VP2|1|2A|U|1798
5VP2|1|2A|G|1799
5VP2|1|2A|C|1800
5VP2|1|2A|G|1801
5VP2|1|2A|A|1802
5VP2|1|2A|A|1803
5VP2|1|2A|C|1804
*
5VP2|1|2A|G|1813
5VP2|1|2A|G|1814
5VP2|1|2A|A|1815
5VP2|1|2A|G|1816
5VP2|1|2A|G|1817
5VP2|1|2A|U|1818
5VP2|1|2A|A|1819
5VP2|1|2A|U|1820
5VP2|1|2A|A|1821

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA