J4_9DFD_027

3D structure

PDB id

9DFD (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with lasso peptide lariocidin B, mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.60A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

GAGUAACG*UC*GUAG*CC

Length

16 nucleotides

Bulged bases

9DFD|1|2a|C|121

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_9DFD_027 not in the Motif Atlas

Homologous match to J4_4LFB_001

Geometric discrepancy: 0.0641

The information below is about J4_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_90044.1

Basepair signature

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

Number of instances in this motif group

2

Unit IDs

9DFD|1|2a|G|115
9DFD|1|2a|A|116
9DFD|1|2a|G|117
9DFD|1|2a|U|118
9DFD|1|2a|A|119
9DFD|1|2a|A|120
9DFD|1|2a|C|121
9DFD|1|2a|G|122
*
9DFD|1|2a|U|239
9DFD|1|2a|C|240
*
9DFD|1|2a|G|286
9DFD|1|2a|U|287
9DFD|1|2a|A|288
9DFD|1|2a|G|289
*
9DFD|1|2a|C|311
9DFD|1|2a|C|312

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2p

30S ribosomal protein S16

Chain 2q

30S ribosomal protein S17