Structure of PDB 5wfk Chain z

Receptor sequence

>5wfkz (length=393) Species: 83333 (Escherichia coli K-12)

SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFNQID
NAPEEKARGITINTSHVEYDTPTRHYAHVDCPGAADYVKNMITGAAQMDG
AILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVE
MEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIP
EPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKET
QKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKP
HTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMV
MPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

3D structure

• PDB: 5wfk Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.
• Chain: z
• 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	z	S221 G222 R223 R279	S221 G222 R223 R279
BS02	rna	z	S1 P53 N63 K89 I220 S221 R223 E259 R262 R288 R318 H319 T320 G325 Y326 R327 Q329 T338 I363 H364 E378	S1 P53 N63 K89 I220 S221 R223 E259 R262 R288 R318 H319 T320 G325 Y326 R327 Q329 T338 I363 H364 E378
BS03	PHE	z	H66 F218 F261 N273	H66 F218 F261 N273
BS04	GTP	z	V20 D21 G23 K24 T25 T26 I60 T61 P82 N135 M139 S173 A174 L175	V20 D21 G23 K24 T25 T26 I60 T61 P82 N135 M139 S173 A174 L175

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0097216 guanosine tetraphosphate binding

Biological Process

• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0046677 response to antibiotic

Cellular Component

• GO:0005737 cytoplasm
• GO:0005886 plasma membrane
• GO:0032045 guanyl-nucleotide exchange factor complex

External links

• PDB: RCSB:5wfk, PDBe:5wfk, PDBj:5wfk
• PDBsum: 5wfk
• PubMed: 29733411
• UniProt: P0CE48|EFTU2_ECOLI Elongation factor Tu 2 (Gene Name=tufB)