IL_5VP2_235

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

CGUAAC*GGAGAAG

Length

13 nucleotides

Bulged bases

5VP2|1|2A|G|1699

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_235 not in the Motif Atlas

Homologous match to IL_9DFE_068

Geometric discrepancy: 0.1235

The information below is about IL_9DFE_068

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_20700.1

Basepair signature

cWW-tSH-L-R-tHH-tHS-cWW

Number of instances in this motif group

10

Unit IDs

5VP2|1|2A|C|1686
5VP2|1|2A|G|1687
5VP2|1|2A|U|1688
5VP2|1|2A|A|1689
5VP2|1|2A|A|1690
5VP2|1|2A|C|1691
*
5VP2|1|2A|G|1696
5VP2|1|2A|G|1697
5VP2|1|2A|A|1698
5VP2|1|2A|G|1699
5VP2|1|2A|A|1700
5VP2|1|2A|A|1701
5VP2|1|2A|G|1702

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA