Structure of PDB 8cgv Chain d

Receptor sequence

>8cgvd (length=207) Species: 679895 (Escherichia coli BW25113)

IGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVT
TGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELF
ADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQT
PGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDL
IVKPAVK

3D structure

• PDB: 8cgv Structural conservation of antibiotic interaction with ribosomes.
• Chain: d
• Resolution: 1.66 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	d	M11 R13 P23 Q36 N42 D43 Y45 Q49 K56 R59 T61 K62 P63 E64 G66 H67 K70 L79 E81 R83 S113 K114 G115 K116 G117 F118 G120 K123 R124 N126 F127 R128 T129 Q130 A132 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 X150 T151 P152 G153 K154 V155 F156 K157 G158 K159 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 L175 K190 A192 V193 P194 G195 A196 T197 K208	M10 R12 P22 Q35 N41 D42 Y44 Q48 K55 R58 T60 K61 P62 E63 G65 H66 K69 L78 E80 R82 S112 K113 G114 K115 G116 F117 G119 K122 R123 N125 F126 R127 T128 Q129 A131 T132 H133 G134 N135 S136 L137 S138 H139 R140 P142 G143 S144 I145 G146 Q147 N148 X149 T150 P151 G152 K153 V154 F155 K156 G157 K158 M160 A161 Q163 N166 R168 V169 T170 Q172 S173 L174 K189 A191 V192 P193 G194 A195 T196 K207

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:8cgv, PDBe:8cgv, PDBj:8cgv
• PDBsum: 8cgv
• PubMed: 37550453
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)