J5_9DFD_015

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

GCAAGUUGG*UG*CC*GUGAACAGG*CGC

Length

25 nucleotides

Bulged bases

9DFD|1|2A|G|1758, 9DFD|1|2A|G|1763

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_9DFD_015 not in the Motif Atlas

Homologous match to J5_9DFE_005

Geometric discrepancy: 0.0668

The information below is about J5_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_99177.1

Basepair signature

cWW-F-F-F-cWW-F-F-F-F-F-F-F-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

10

Unit IDs

9DFD|1|2A|G|1674
9DFD|1|2A|C|1675
9DFD|1|2A|A|1676
9DFD|1|2A|A|1677
9DFD|1|2A|G|1678
9DFD|1|2A|U|1679
9DFD|1|2A|U|1680
9DFD|1|2A|G|1681
9DFD|1|2A|G|1682
*
9DFD|1|2A|U|1706
9DFD|1|2A|G|1707
*
9DFD|1|2A|C|1751
9DFD|1|2A|C|1752
*
9DFD|1|2A|G|1756
9DFD|1|2A|U|1757
9DFD|1|2A|G|1758
9DFD|1|2A|A|1759
9DFD|1|2A|A|1760
9DFD|1|2A|C|1761
9DFD|1|2A|A|1762
9DFD|1|2A|G|1763
9DFD|1|2A|G|1764
*
9DFD|1|2A|C|1988
9DFD|1|2A|G|1989
9DFD|1|2A|C|1990

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2E

50S ribosomal protein L3

Chain 2O

50S ribosomal protein L14

Chain 2T

50S ribosomal protein L19

Chain 2a

Small subunit ribosomal RNA; SSU rRNA