Structure of PDB 6wd2 Chain 8

Receptor sequence

>6wd28 (length=392) Species: 562 (Escherichia coli)

SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQID
NAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDG
AILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVE
MEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIP
EPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKET
QKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKP
HTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMV
MPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVL

3D structure

• PDB: 6wd2 Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading.
• Chain: 8
• Resolution: 3.6 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	8	G223 R224 G225 T257 R280	G222 R223 G224 T256 R279
BS02	rna	8	N52 P54 Y88 F219 S220 I221 V227 G258 E260 R263 R319 H320 T321 G326 Y327 R328 Q330 D337 T339 G380	N51 P53 Y87 F218 S219 I220 V226 G257 E259 R262 R318 H319 T320 G325 Y326 R327 Q329 D336 T338 G379
BS03	PHE	8	H67 F219 M261 F262 N274	H66 F218 M260 F261 N273
BS04	GTP	8	H20 V21 D22 H23 G24 K25 T26 T27 F47 I61 T62 G84 H85 N136 K137 D139 M140 S174 A175 L176	H19 V20 D21 H22 G23 K24 T25 T26 F46 I60 T61 G83 H84 N135 K136 D138 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:6wd2, PDBe:6wd2, PDBj:6wd2
• PDBsum: 6wd2
• PubMed: 32612237
• UniProt: P0CE47|EFTU1_ECOLI Elongation factor Tu 1 (Gene Name=tufA)