Structure of PDB 8ekb Chain 2e

Receptor sequence

>8ekb2e (length=148) Species: 300852 (Thermus thermophilus HB8)

DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLA
VQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGA
VPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLR

3D structure

• PDB: 8ekb Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.
• Chain: 2e
• 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	2e	R14 T16 A17 R18 M19 Q20 A21 G22 R24 R25 K47 K57 G85 A94 A95 T98 I101 A102 R107 L119 T120 K121 E122 L123 S125 R126 N127	R10 T12 A13 R14 M15 Q16 A17 G18 R20 R21 K43 K53 G81 A90 A91 T94 I97 A98 R103 L115 T116 K117 E118 L119 S121 R122 N123
BS02	MG	2e	E68 D147	E64 D143

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• 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: Q5SHQ5|RS5_THET8 Small ribosomal subunit protein uS5 (Gene Name=rpsE)