IL_5VP2_361

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

GGACG*CGGUAC

Length

11 nucleotides

Bulged bases

None detected

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_361 not in the Motif Atlas

Homologous match to IL_4LFB_018

Geometric discrepancy: 0.15

The information below is about IL_4LFB_018

Detailed Annotation

6x5 Sarcin-Ricin; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_82100.1

Basepair signature

cWW-tWW-cSH-tWH-tHS-cWW

Number of instances in this motif group

3

Unit IDs

5VP2|1|2a|G|446
5VP2|1|2a|G|447
5VP2|1|2a|A|448
5VP2|1|2a|C|449
5VP2|1|2a|G|450
*
5VP2|1|2a|C|483
5VP2|1|2a|G|484
5VP2|1|2a|G|485
5VP2|1|2a|U|486
5VP2|1|2a|A|487
5VP2|1|2a|C|488

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2d

30S ribosomal protein S4

Chain 2p

30S ribosomal protein S16