HL_9D7T_105

3D structure

PDB id

9D7T (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Api137 antimicrobial peptide, mRNA, A-site release factor 1, and deacylated P-site and E-site tRNAphe at 2.70A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.7 Å

Loop

Sequence

G(5MU)(PSU)CGAUUC

Length

9 nucleotides

Bulged bases

None detected

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_9D7T_105 not in the Motif Atlas

Homologous match to HL_6PMO_005

Geometric discrepancy: 0.2241

The information below is about HL_6PMO_005

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_28252.4

Basepair signature

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

Number of instances in this motif group

143

Unit IDs

9D7T|1|1y|G|53
9D7T|1|1y|5MU|54
9D7T|1|1y|PSU|55
9D7T|1|1y|C|56
9D7T|1|1y|G|57
9D7T|1|1y|A|58
9D7T|1|1y|U|59
9D7T|1|1y|U|60
9D7T|1|1y|C|61

Current chains

Chain 1y

P-site and E-site Deacylated tRNAphe

Nearby chains

Chain 1A

Large subunit ribosomal RNA; LSU rRNA