IL_9D7S_242

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

CCGG*CG

Length

6 nucleotides

Bulged bases

9D7S|1|2A|C|1838

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

IL_9D7S_242 not in the Motif Atlas

Homologous match to IL_9DFE_071

Geometric discrepancy: 0.0824

The information below is about IL_9DFE_071

Detailed Annotation

Minor groove platform, major groove intercalation

Broad Annotation

Minor groove platform, major groove intercalation

Motif group

IL_95583.2

Basepair signature

cWW-L-cWW

Number of instances in this motif group

11

Unit IDs

9D7S|1|2A|C|1837
9D7S|1|2A|C|1838
9D7S|1|2A|G|1839
9D7S|1|2A|G|1840
*
9D7S|1|2A|C|1902
9D7S|1|2A|G|1903

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA