Structure of PDB 6kcn Chain D

Receptor sequence
>6kcnD (length=502) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence]
VDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEH
LEDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNF
AECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYKD
TEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMN
LIAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVF
RNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKIS
YNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMI
NIIKEHKIELPPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAK
YHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFKLQQKDREKGDT
EAAQLDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMR
PA
3D structure
PDB6kcn Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase.
ChainD
Resolution2.2 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) R251 E253 T258 H259 E420 N423 R479
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 D5F D R330 E332 H338 N339 F342 L502 G554 L555 R559 R251 E253 H259 N260 F263 L422 G474 L475 R479 MOAD: ic50=276nM
BS02 LYS D E308 E346 Y348 N503 Y505 E507 G552 E229 E267 Y269 N423 Y425 E427 G472
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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Biological Process
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Cellular Component
External links
PDB RCSB:6kcn, PDBe:6kcn, PDBj:6kcn
PDBsum6kcn
PubMed32195573
UniProtW7JP72

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