J5_8VTX_004

3D structure

PDB id

8VTX (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in complex with macrolone MCX-128, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.4 Å

Loop

Sequence

CGACUC*GGAC*GUUC*GC*GCGAAUG

Length

23 nucleotides

Bulged bases

8VTX|1|1A|U|1255

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

J5_8VTX_004 not in the Motif Atlas

Homologous match to J5_9DFE_004

Geometric discrepancy: 0.0445

The information below is about J5_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_74302.6

Basepair signature

cWW-tSH-tSS-tHW-F-cHS-F-tWS-cWW-cWW-F-cWW-cWW-F

Number of instances in this motif group

4

Unit IDs

8VTX|1|1A|C|584
8VTX|1|1A|G|585
8VTX|1|1A|A|586
8VTX|1|1A|C|587
8VTX|1|1A|U|588
8VTX|1|1A|C|589
*
8VTX|1|1A|G|668
8VTX|1|1A|G|669
8VTX|1|1A|A|670
8VTX|1|1A|C|671
*
8VTX|1|1A|G|809
8VTX|1|1A|U|810
8VTX|1|1A|U|811
8VTX|1|1A|C|812
*
8VTX|1|1A|G|1195
8VTX|1|1A|C|1196
*
8VTX|1|1A|G|1250
8VTX|1|1A|C|1251
8VTX|1|1A|G|1252
8VTX|1|1A|A|1253
8VTX|1|1A|A|1254
8VTX|1|1A|U|1255
8VTX|1|1A|G|1256

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 18

50S ribosomal protein L35

Chain 1F

50S ribosomal protein L4

Chain 1P

50S ribosomal protein L15

Chain 1U

50S ribosomal protein L20

Chain 1V

50S ribosomal protein L21