Structure of PDB 4www Chain YD

Receptor sequence

>4wwwYD (length=209) Species: 83333 (Escherichia coli K-12)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

3D structure

• PDB: 4www Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.
• Chain: YD
• Resolution: 3.1 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	YD	M11 R13 P23 Q36 N42 D43 Y45 K56 R59 T61 K62 P63 H67 K70 L79 W80 E81 R83 K114 G115 K116 G117 F118 G120 K123 F127 R128 T129 Q130 D131 A132 T133 H134 N136 S137 L138 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 K154 V155 F156 K157 G158 K159 M161 A162 G163 Q164 N167 R169 T171 Q173 S174 K190 G191 A192 P194 T197 K208	M11 R13 P23 Q36 N42 D43 Y45 K56 R59 T61 K62 P63 H67 K70 L79 W80 E81 R83 K114 G115 K116 G117 F118 G120 K123 F127 R128 T129 Q130 D131 A132 T133 H134 N136 S137 L138 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 K154 V155 F156 K157 G158 K159 M161 A162 G163 Q164 N167 R169 T171 Q173 S174 K190 G191 A192 P194 T197 K208

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• 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:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4www, PDBe:4www, PDBj:4www
• PDBsum: 4www
• PubMed: 20855725
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)