Structure of PDB 5dfe Chain XY

Receptor sequence

>5dfeXY (length=357) Species: 83333 (Escherichia coli K-12)

PVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQA
LGKERSSLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDA
LEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLERMYLRW
AESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKS
PFDSGGRRHTSFSSAFVYPEVDDDIDIEINPADLRIDVYRTSGAGGQHVN
RTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNA
EKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQ
FIEASLK

3D structure

• PDB: 5dfe Uniformity of Peptide Release Is Maintained by Methylation of Release Factors.
• Chain: XY
• Resolution: 3.09998 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	XY	G250 G251 H253 R278	G245 G246 H248 R273
BS02	rna	XY	G137 G138 E140 V202 S205 F207 D208 R212 R213 H214 T215	G132 G133 E135 V197 S200 F202 D203 R207 R208 H209 T210
BS03	rna	XY	W47 Q54 K58 Q133 S219 Y244 R245 S247 G248 G250 G251 Q252 H253 V254 N255 R256 T257 E258 S259 R262 Q273 N276 R278 Q280 H281 Q290 Q308 S315 I317	W42 Q49 K53 Q128 S214 Y239 R240 S242 G243 G245 G246 Q247 H248 V249 N250 R251 T252 E253 S254 R257 Q268 N271 R273 Q275 H276 Q285 Q303 S310 I312
BS04	rna	XY	P6 G135 S136 R154 R200 S209 R212 R213 W319 G320 Q322 D329 D330 S331 R332	P1 G130 S131 R149 R195 S204 R207 R208 W314 G315 Q317 D324 D325 S326 R327
BS05	MG	XY	S169 K177	S164 K172

Gene Ontology

Molecular Function

• GO:0003747 translation release factor activity
• GO:0016149 translation release factor activity, codon specific

Biological Process

• GO:0006412 translation
• GO:0006415 translational termination
• GO:0075523 viral translational frameshifting

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5dfe, PDBe:5dfe, PDBj:5dfe
• PDBsum: 5dfe
• PubMed: 27681416
• UniProt: P07012|RF2_ECOLI Peptide chain release factor RF2 (Gene Name=prfB)