Structure of PDB 4v5b Chain AD

Receptor sequence

>4v5bAD (length=209) Species: 562 (Escherichia coli)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

3D structure

• PDB: 4v5b A Peptide Deformylase-Ribosome Complex Reveals Mechanism of Nascent Chain Processing.
• Chain: AD
• Resolution: 3.74 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	AD	G10 I22 A41 N42 K55 N58 T61 K62 A65 G66 F68 R77 W80 F82 K114 G115 K116 G117 F118 A119 G120 R124 F127 R128 T129 Q130 H134 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 V193 G195 T197 A209	G10 I22 A41 N42 K55 N58 T61 K62 A65 G66 F68 R77 W80 F82 K114 G115 K116 G117 F118 A119 G120 R124 F127 R128 T129 Q130 H134 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 Q148 N149 Q150 T151 P152 G153 K154 V155 F156 K157 G158 M161 A162 Q164 N167 R169 V170 T171 Q173 S174 V193 G195 T197 A209

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:4v5b, PDBe:4v5b, PDBj:4v5b
• PDBsum: 4v5b
• PubMed: 18288106
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)