J4_9D7S_025

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

GAGUAACG*UC*GUAG*CC

Length

16 nucleotides

Bulged bases

9D7S|1|2a|C|121

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

J4_9D7S_025 not in the Motif Atlas

Homologous match to J4_4LFB_001

Geometric discrepancy: 0.0653

The information below is about J4_4LFB_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_35578.3

Basepair signature

cWW-F-cWW-F-F-F-tHW-F-cWW-cWW

Number of instances in this motif group

2

Unit IDs

9D7S|1|2a|G|115
9D7S|1|2a|A|116
9D7S|1|2a|G|117
9D7S|1|2a|U|118
9D7S|1|2a|A|119
9D7S|1|2a|A|120
9D7S|1|2a|C|121
9D7S|1|2a|G|122
*
9D7S|1|2a|U|239
9D7S|1|2a|C|240
*
9D7S|1|2a|G|286
9D7S|1|2a|U|287
9D7S|1|2a|A|288
9D7S|1|2a|G|289
*
9D7S|1|2a|C|311
9D7S|1|2a|C|312

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2p

30S ribosomal protein S16

Chain 2q

30S ribosomal protein S17