J4_5VP2_021

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

UC*GGUUAG*CU*ACCCGUA

Length

17 nucleotides

Bulged bases

5VP2|1|2A|U|1341

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

J4_5VP2_021 not in the Motif Atlas

Homologous match to J4_9DFE_005

Geometric discrepancy: 0.0848

The information below is about J4_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_10313.5

Basepair signature

cWW-cWW-tHW-F-F-F-F-F-F-cWW-cWW

Number of instances in this motif group

5

Unit IDs

5VP2|1|2A|U|1313
5VP2|1|2A|C|1314
*
5VP2|1|2A|G|1338
5VP2|1|2A|G|1339
5VP2|1|2A|U|1340
5VP2|1|2A|U|1341
5VP2|1|2A|A|1342
5VP2|1|2A|G|1343
*
5VP2|1|2A|C|1404
5VP2|1|2A|U|1405
*
5VP2|1|2A|A|1597
5VP2|1|2A|C|1598
5VP2|1|2A|C|1599
5VP2|1|2A|C|1600
5VP2|1|2A|G|1601
5VP2|1|2A|U|1602
5VP2|1|2A|A|1603

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2X

50S ribosomal protein L23