IL_5VP2_363

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

G(4OC)C(5MC)*G(UR3)AAC

Length

9 nucleotides

Bulged bases

None detected

QA status

Modified nucleotides: 4OC, 5MC, UR3

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_363 not in the Motif Atlas

Homologous match to IL_4LFB_068

Geometric discrepancy: 0.1015

The information below is about IL_4LFB_068

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_65718.4

Basepair signature

cWW-cSH-cWS-cWW-cWW

Number of instances in this motif group

4

Unit IDs

5VP2|1|2a|G|1401
5VP2|1|2a|4OC|1402
5VP2|1|2a|C|1403
5VP2|1|2a|5MC|1404
*
5VP2|1|2a|G|1497
5VP2|1|2a|UR3|1498
5VP2|1|2a|A|1499
5VP2|1|2a|A|1500
5VP2|1|2a|C|1501

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2A

Large subunit ribosomal RNA; LSU rRNA

Chain 2v

mRNA

Chain 2x

Transfer RNA; tRNA