HL_9D0I_210

3D structure

PDB id

9D0I (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Se-cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.45A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.45 Å

Loop

Sequence

G(5MU)(PSU)CGAUUC

Length

9 nucleotides

Bulged bases

9D0I|1|2y|C|56

QA status

Modified nucleotides: 5MU, PSU

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_9D0I_210 not in the Motif Atlas

Geometric match to HL_5HR6_003

Geometric discrepancy: 0.3915

The information below is about HL_5HR6_003

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

9D0I|1|2y|G|53
9D0I|1|2y|5MU|54
9D0I|1|2y|PSU|55
9D0I|1|2y|C|56
9D0I|1|2y|G|57
9D0I|1|2y|A|58
9D0I|1|2y|U|59
9D0I|1|2y|U|60
9D0I|1|2y|C|61

Current chains

Chain 2y

A-site and E-site Deacylated tRNAphe

Nearby chains

Chain 2A

Large subunit ribosomal RNA; LSU rRNA