J4_9D7S_014

3D structure

PDB id

9D7S (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Api antimicrobial peptide, mRNA, A-site release factor 1, and deacylated P-site and E-site tRNAphe at 2.85A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.85 Å

Loop

Sequence

A(4SU)AG*CAG*CGU(G7M)UCC*GU

Length

16 nucleotides

Bulged bases

9D7S|1|1y|4SU|8, 9D7S|1|1y|U|47, 9D7S|1|1y|C|48

QA status

Modified nucleotides: 4SU, G7M

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

J4_9D7S_014 not in the Motif Atlas

Homologous match to J4_3WQY_001

Geometric discrepancy: 0.2203

The information below is about J4_3WQY_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_70449.29

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

54

Unit IDs

9D7S|1|1y|A|7
9D7S|1|1y|4SU|8
9D7S|1|1y|A|9
9D7S|1|1y|G|10
*
9D7S|1|1y|C|25
9D7S|1|1y|A|26
9D7S|1|1y|G|27
*
9D7S|1|1y|C|43
9D7S|1|1y|G|44
9D7S|1|1y|U|45
9D7S|1|1y|G7M|46
9D7S|1|1y|U|47
9D7S|1|1y|C|48
9D7S|1|1y|C|49
*
9D7S|1|1y|G|65
9D7S|1|1y|U|66

Current chains

Chain 1y

P-site and E-site Deacylated tRNAphe

Nearby chains

Chain 16

50S ribosomal protein L33

Chain 1g

30S ribosomal protein S7