J3_9D7S_038

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

9D7S|1|2A|U|504, 9D7S|1|2A|G|508

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

J3_9D7S_038 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0585

The information below is about J3_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_92134.2

Basepair signature

cWW-cWW-cWW-F-tWH-cSS-tSS-tSH-tSH-tWW-tHH-tWH-tWW-F-F-cSS-cSW-F-tHS-cWW

Number of instances in this motif group

6

Unit IDs

9D7S|1|2A|G|30
9D7S|1|2A|C|31
*
9D7S|1|2A|G|474
9D7S|1|2A|U|475
9D7S|1|2A|G|476
9D7S|1|2A|A|477
9D7S|1|2A|A|478
9D7S|1|2A|A|479
9D7S|1|2A|A|480
9D7S|1|2A|G|481
9D7S|1|2A|A|482
9D7S|1|2A|A|483
9D7S|1|2A|C|484
*
9D7S|1|2A|G|496
9D7S|1|2A|A|497
9D7S|1|2A|G|498
9D7S|1|2A|U|499
9D7S|1|2A|G|500
9D7S|1|2A|A|501
9D7S|1|2A|A|502
9D7S|1|2A|A|503
9D7S|1|2A|U|504
9D7S|1|2A|A|505
9D7S|1|2A|G|506
9D7S|1|2A|A|507
9D7S|1|2A|G|508
9D7S|1|2A|C|509
9D7S|1|2A|C|510

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22

Chain 2Y

50S ribosomal protein L24