Structure of PDB 4v54 Chain DO

Receptor sequence

>4v54DO (length=116) Species: 562 (Escherichia coli)

DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAA
STVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHG
RVQALADAAREAGLQF

3D structure

• PDB: 4v54 Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.
• Chain: DO
• Resolution: 3.3 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	DO	K3 K4 R15 R25 H29 R30 T31 P32 R33 H34 Y36 Q38 I40 G44 S45 E46 V47 V54 Y64 N67 K68 Q98 H100 G101 R102	K2 K3 R14 R24 H28 R29 T30 P31 R32 H33 Y35 Q37 I39 G43 S44 E45 V46 V53 Y63 N66 K67 Q97 H99 G100 R101
BS02	rna	DO	R10 T12 R13 R16 K17 L18 L21 F92 R94 Y99 R111 F117	R9 T11 R12 R15 K16 L17 L20 F91 R93 Y98 R110 F116

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 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:4v54, PDBe:4v54, PDBj:4v54
• PDBsum: 4v54
• PubMed: 17660832
• UniProt: P0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)