Structure of PDB 6b4v Chain JA

Receptor sequence

>6b4vJA (length=258) Species: 562 (Escherichia coli)

LPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMS
ASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSA
CTVAVMPELPDAELPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLP
TGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGS
GDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQA
DQLAALSE

3D structure

• PDB: 6b4v Mechanism of Inhibition of Translation Termination by Blasticidin S.
• Chain: JA
• Resolution: 3.4 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 G120 R137 K160 R183 G194 I196 D302 R303 S304 R316 Y327	G18 T19 G20 R37 K60 R83 G94 I96 D202 R203 S204 R216 Y227
BS02	rna	JA	R228 S230 A232 G234 Q235 H236 N238 T239 T240 D241 R245 Q263 H264	R128 S130 A132 G134 Q135 H136 N138 T139 T140 D141 R145 Q163 H164
BS03	rna	JA	G120 G121 D122 E123 T190 G194 R195 I196 H197 T198	G20 G21 D22 E23 T90 G94 R95 I96 H97 T98
BS04	rna	JA	E155 H156 G233 H236 E260 R261	E55 H56 G133 H136 E160 R161
BS05	MG	JA	A289 T293	A189 T193

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:6b4v, PDBe:6b4v, PDBj:6b4v
• PDBsum: 6b4v
• PubMed: 29366636
• UniProt: P0A7I0|RF1_ECOLI Peptide chain release factor RF1 (Gene Name=prfA)