HL_5VP2_033

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

GGUCGUC

Length

7 nucleotides

Bulged bases

5VP2|1|1A|G|1371, 5VP2|1|1A|U|1375

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

HL_5VP2_033 not in the Motif Atlas

Homologous match to HL_9DFE_032

Geometric discrepancy: 0.0538

The information below is about HL_9DFE_032

Detailed Annotation

Pseudoknot geometry with 3' bulge

Broad Annotation

No text annotation

Motif group

HL_49081.1

Basepair signature

cWW-F-F-F

Number of instances in this motif group

17

Unit IDs

5VP2|1|1A|G|1370
5VP2|1|1A|G|1371
5VP2|1|1A|U|1372
5VP2|1|1A|C|1373
5VP2|1|1A|G|1374
5VP2|1|1A|U|1375
5VP2|1|1A|C|1376

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1R

50S ribosomal protein L17

Chain 1W

50S ribosomal protein L22