J3_9DFD_039

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

9DFD|1|2A|U|504, 9DFD|1|2A|G|508

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

J3_9DFD_039 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0587

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.1

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

9

Unit IDs

9DFD|1|2A|G|30
9DFD|1|2A|C|31
*
9DFD|1|2A|G|474
9DFD|1|2A|U|475
9DFD|1|2A|G|476
9DFD|1|2A|A|477
9DFD|1|2A|A|478
9DFD|1|2A|A|479
9DFD|1|2A|A|480
9DFD|1|2A|G|481
9DFD|1|2A|A|482
9DFD|1|2A|A|483
9DFD|1|2A|C|484
*
9DFD|1|2A|G|496
9DFD|1|2A|A|497
9DFD|1|2A|G|498
9DFD|1|2A|U|499
9DFD|1|2A|G|500
9DFD|1|2A|A|501
9DFD|1|2A|A|502
9DFD|1|2A|A|503
9DFD|1|2A|U|504
9DFD|1|2A|A|505
9DFD|1|2A|G|506
9DFD|1|2A|A|507
9DFD|1|2A|G|508
9DFD|1|2A|C|509
9DFD|1|2A|C|510

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22

Chain 2Y

50S ribosomal protein L24