Structure of PDB 8ifc Chain i

Receptor sequence

>8ifci (length=142) Species: 562 (Escherichia coli)

MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDT
GDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERV
IEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI

3D structure

• PDB: 8ifc Direct visualization of ribosomes in the cell-free system revealed the functional evolution of aminoglycoside.
• Chain: i
• Resolution: 2.9 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	i	K2 T3 K7 E9 W15 T24 L25 G26 R27 T30 R37 K39 H47 T65 K68 Y75 H76 H77 T78 H80 I81 G82 I84 R96 E102 A104 G107 M108 P110 K111 P113 L114 R116 R120 N131 H132 A134 Q135 Q136	K2 T3 K7 E9 W15 T24 L25 G26 R27 T30 R37 K39 H47 T65 K68 Y75 H76 H77 T78 H80 I81 G82 I84 R96 E102 A104 G107 M108 P110 K111 P113 L114 R116 R120 N131 H132 A134 Q135 Q136

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0048027 mRNA 5'-UTR binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ifc, PDBe:8ifc, PDBj:8ifc
• PDBsum: 8ifc
• PubMed: 38227611
• UniProt: P0AA10|RL13_ECOLI Large ribosomal subunit protein uL13 (Gene Name=rplM)