Structure of PDB 5j4d Chain JA

Receptor sequence

>5j4dJA (length=258) Species: 83333 (Escherichia coli K-12)

LPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMS
ASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSA
CTVAVMPELPDAELPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLP
TGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGS
GDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQA
DQLAALSE

3D structure

• PDB: 5j4d Structural Basis for Translation Termination on a Pseudouridylated Stop Codon.
• Chain: JA
• 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	JA	G118 T119 G121 R133 R183 Q185 Q193 R195 R303 Q314	G18 T19 G21 R33 R83 Q85 Q93 R95 R203 Q214
BS02	rna	JA	R228 S229 S230 G231 A232 G233 G234 Q235 H236 V237 N238 T239 T240 D241 S242 R245 E256 D259 R261 Q263 R277 R295	R128 S129 S130 G131 A132 G133 G134 Q135 H136 V137 N138 T139 T140 D141 S142 R145 E156 D159 R161 Q163 R177 R195
BS03	rna	JA	G120 E123 T190 R195 I196 H197 T198	G20 E23 T90 R95 I96 H97 T98
BS04	rna	JA	E155 G233 G234 Q235 E260 R261 K265	E55 G133 G134 Q135 E160 R161 K165
BS05	MG	JA	R183 H320	R83 H220
BS06	MG	JA	L214 I217 H248	L114 I117 H148

Gene Ontology

Molecular Function

• GO:0003747 translation release factor activity
• GO:0005515 protein binding
• GO:0016149 translation release factor activity, codon specific
• GO:0043022 ribosome binding

Biological Process

• GO:0006412 translation
• GO:0006415 translational termination

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5j4d, PDBe:5j4d, PDBj:5j4d
• PDBsum: 5j4d
• PubMed: 27107638
• UniProt: P0A7I0|RF1_ECOLI Peptide chain release factor RF1 (Gene Name=prfA)