Structure of PDB 8syl Chain O

Receptor sequence

>8sylO (length=136) Species: 562 (Escherichia coli)

MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAAR
RAMTRAVKRQGKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGK
VLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM

3D structure

• PDB: 8syl Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.
• Chain: O
• 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	O	R50 R51 R55 R59	R50 R51 R55 R59
BS02	rna	O	P4 K5 R6 K8 F9 R10 K11 M12 H13 K14 G15 R16 Q22 G23 F28 R40 R44 Q45 A48 R55 K62 W64 R66 F68 D70 K76 A79 V80 X81 X82 G83 K84 G85 K86 K100 A122 K123 P125	P4 K5 R6 K8 F9 R10 K11 M12 H13 K14 G15 R16 Q22 G23 F28 R40 R44 Q45 A48 R55 K62 W64 R66 F68 D70 K76 A79 V80 X81 X82 G83 K84 G85 K86 K100 A122 K123 P125
BS03	rna	O	R16 N17 R18 G19 R38	R16 N17 R18 G19 R38

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:8syl, PDBe:8syl, PDBj:8syl
• PDBsum: 8syl
• PubMed: 37537169
• UniProt: P0ADY7|RL16_ECOLI Large ribosomal subunit protein uL16 (Gene Name=rplP)