Structure of PDB 8rpy Chain M

Receptor sequence

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

MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAAR
RAMTRAVKRQGKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGK
VLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM

3D structure

• PDB: 8rpy Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88.
• Chain: M
• Resolution: 2.64 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	M	K5 R6 K8 F9 R10 K11 M12 H13 K14 G15 R16 Q22 F28 R40 R44 Q45 R55 W64 R66 F68 D70 E75 K76 A79 R81 M82 G83 K84 G85 K86 A122 K123 P125	K5 R6 K8 F9 R10 K11 M12 H13 K14 G15 R16 Q22 F28 R40 R44 Q45 R55 W64 R66 F68 D70 E75 K76 A79 R81 M82 G83 K84 G85 K86 A122 K123 P125
BS02	rna	M	R18 R38	R18 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:8rpy, PDBe:8rpy, PDBj:8rpy
• PDBsum: 8rpy
• PubMed: 38730238
• UniProt: P0ADY7|RL16_ECOLI Large ribosomal subunit protein uL16 (Gene Name=rplP)