Structure of PDB 5gad Chain D

Receptor sequence

>5gadD (length=209) Species: 562 (Escherichia coli)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

3D structure

• PDB: 5gad Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.
• Chain: D
• Resolution: 3.7 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 T12 R13 P23 Q36 N42 Y45 Q49 K56 R59 T61 K62 P63 E64 G66 H67 K70 E81 R83 K114 G115 K116 G117 F118 G120 K123 R124 F127 R128 T129 Q130 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 K154 V155 F156 K157 G158 K159 M161 A162 Q164 R169 T171 Q173 S174 K190 A192 V193 T197 K208	M11 T12 R13 P23 Q36 N42 Y45 Q49 K56 R59 T61 K62 P63 E64 G66 H67 K70 E81 R83 K114 G115 K116 G117 F118 G120 K123 R124 F127 R128 T129 Q130 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 K154 V155 F156 K157 G158 K159 M161 A162 Q164 R169 T171 Q173 S174 K190 A192 V193 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:5gad, PDBe:5gad, PDBj:5gad
• PDBsum: 5gad
• PubMed: 26804923
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)