Structure of PDB 6ka6 Chain B

Receptor sequence
>6ka6B (length=504) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence]
DPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHL
EDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFA
ECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYGLK
DTEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMM
NLIAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKV
FRNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKI
SYNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKM
INIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPL
AKYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFKLQQKDREKG
DTEAAQLDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPT
MRPA
3D structure
PDB6ka6 Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase.
ChainB
Resolution1.891 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) R330 E332 T337 H338 E500 N503 R559
Catalytic site (residue number reindexed from 1) R252 E254 T259 H260 E422 N425 R481
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
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 D4O B R330 E332 H338 N339 F342 E500 L502 G554 R559 R252 E254 H260 N261 F264 E422 L424 G476 R481 MOAD: ic50=221nM
BS02 LYS B E308 E346 Y348 N503 Y505 E507 G552 E230 E268 Y270 N425 Y427 E429 G474
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Cellular Component
External links
PDB RCSB:6ka6, PDBe:6ka6, PDBj:6ka6
PDBsum6ka6
PubMed32195573
UniProtW7JP72

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