Structure of PDB 8ekb Chain 1i

Receptor sequence

>8ekb1i (length=127) Species: 300852 (Thermus thermophilus HB8)

EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLR
AVDALGHFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGF
LTRDARVVERKKYGKHKARRAPQYSKR

3D structure

• PDB: 8ekb Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.
• Chain: 1i
• Resolution: 2.7 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	1i	Q3 Y5 T7 R9 K11 E12 V14 R16 F18 R20 Y36 Q38 Y62 R66 G67 G68 G69 K70 S71 G72 Q73 R83 K97 T103 R104 R107 V108 V109 E110 R111 K112 K113 Y114 G115 K118 R120 R121 A122 Q124 Y125 K127 R128	Q2 Y4 T6 R8 K10 E11 V13 R15 F17 R19 Y35 Q37 Y61 R65 G66 G67 G68 K69 S70 G71 Q72 R82 K96 T102 R103 R106 V107 V108 E109 R110 K111 K112 Y113 G114 K117 R119 R120 A121 Q123 Y124 K126 R127
BS02	rna	1i	K127 R128	K126 R127

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ekb, PDBe:8ekb, PDBj:8ekb
• PDBsum: 8ekb
• PubMed: 36546783
• UniProt: P80374|RS9_THET8 Small ribosomal subunit protein uS9 (Gene Name=rpsI)