Structure of PDB 4v6d Chain DD

Receptor sequence

>4v6dDD (length=209) Species: 83333 (Escherichia coli K-12)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

3D structure

• PDB: 4v6d Structures of the ribosome in intermediate States of ratcheting.
• Chain: DD
• Resolution: 3.814 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	DD	M11 P23 Q36 N42 Y45 K56 R59 T61 K62 P63 G66 H67 K70 L79 W80 E81 R83 S113 K114 G115 K116 G117 F118 G120 K123 R124 N126 F127 R128 T129 Q130 D131 A132 T133 H134 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 G153 K154 V155 K157 K159 K160 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 K190 G191 P194 G195 T197 K208	M11 P23 Q36 N42 Y45 K56 R59 T61 K62 P63 G66 H67 K70 L79 W80 E81 R83 S113 K114 G115 K116 G117 F118 G120 K123 R124 N126 F127 R128 T129 Q130 D131 A132 T133 H134 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 G153 K154 V155 K157 K159 K160 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 K190 G191 P194 G195 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:4v6d, PDBe:4v6d, PDBj:4v6d
• PDBsum: 4v6d
• PubMed: 19696352
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)