Structure of PDB 6by1 Chain DO

Receptor sequence

>6by1DO (length=116) Species: 83333 (Escherichia coli K-12)

DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAA
STVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHG
RVQALADAAREAGLQF

3D structure

• PDB: 6by1 Structural evidence for product stabilization by the ribosomal mRNA helicase.
• Chain: DO
• Resolution: 3.94 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	R9 R10 R13 F92 R94 Q98 Y99 F117	R8 R9 R12 F91 R93 Q97 Y98 F116
BS02	rna	DO	K3 K4 R15 R25 H29 R30 T31 R33 H34 Y36 Q38 I40 G44 S45 V47 V54 E55 K63 Y64 N67 K68 F97 H100 R102	K2 K3 R14 R24 H28 R29 T30 R32 H33 Y35 Q37 I39 G43 S44 V46 V53 E54 K62 Y63 N66 K67 F96 H99 R101

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:6by1, PDBe:6by1, PDBj:6by1
• PDBsum: 6by1
• PubMed: 30552154
• UniProt: P0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)