J4_9D7S_001

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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

9D7S|1|1A|U|405

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_001 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.0644

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_45801.6

Basepair signature

cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-F-cWW

Number of instances in this motif group

7

Unit IDs

9D7S|1|1A|C|268
9D7S|1|1A|U|269
*
9D7S|1|1A|G|370
9D7S|1|1A|A|371
9D7S|1|1A|G|372
9D7S|1|1A|U|373
9D7S|1|1A|A|374
9D7S|1|1A|C|375
*
9D7S|1|1A|G|399
9D7S|1|1A|G|400
9D7S|1|1A|A|401
9D7S|1|1A|A|402
9D7S|1|1A|U|403
9D7S|1|1A|C|404
9D7S|1|1A|U|405
9D7S|1|1A|G|406
*
9D7S|1|1A|U|421
9D7S|1|1A|A|422
9D7S|1|1A|A|423
9D7S|1|1A|G|424

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L28

Chain 1I

50S ribosomal protein L9