HL_9DFD_123

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

UAUUGAAGCA

Length

10 nucleotides

Bulged bases

9DFD|1|2A|C|574

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

HL_9DFD_123 not in the Motif Atlas

Homologous match to HL_9DFE_016

Geometric discrepancy: 0.0756

The information below is about HL_9DFE_016

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_33597.3

Basepair signature

cWW-tWH-F-F-F-F-F

Number of instances in this motif group

135

Unit IDs

9DFD|1|2A|U|566
9DFD|1|2A|A|567
9DFD|1|2A|U|568
9DFD|1|2A|U|569
9DFD|1|2A|G|570
9DFD|1|2A|A|571
9DFD|1|2A|A|572
9DFD|1|2A|G|573
9DFD|1|2A|C|574
9DFD|1|2A|A|575

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 25

50S ribosomal protein L32

Chain 2E

50S ribosomal protein L3

Chain 2P

50S ribosomal protein L15

Chain 2V

50S ribosomal protein L21