J4_9D7S_018

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

GGUUC*GGUUAG*CU*ACCCGUAC

Length

21 nucleotides

Bulged bases

9D7S|1|2A|U|1341

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_018 not in the Motif Atlas

Homologous match to J4_9DFE_004

Geometric discrepancy: 0.0678

The information below is about J4_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_69051.6

Basepair signature

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

Number of instances in this motif group

7

Unit IDs

9D7S|1|2A|G|1310
9D7S|1|2A|G|1311
9D7S|1|2A|U|1312
9D7S|1|2A|U|1313
9D7S|1|2A|C|1314
*
9D7S|1|2A|G|1338
9D7S|1|2A|G|1339
9D7S|1|2A|U|1340
9D7S|1|2A|U|1341
9D7S|1|2A|A|1342
9D7S|1|2A|G|1343
*
9D7S|1|2A|C|1404
9D7S|1|2A|U|1405
*
9D7S|1|2A|A|1597
9D7S|1|2A|C|1598
9D7S|1|2A|C|1599
9D7S|1|2A|C|1600
9D7S|1|2A|G|1601
9D7S|1|2A|U|1602
9D7S|1|2A|A|1603
9D7S|1|2A|C|1604

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 27

50S ribosomal protein L34

Chain 2X

50S ribosomal protein L23