Structure of PDB 4ycu Chain A

Receptor sequence

>4ycuA (length=505) Species: 9606 (Homo sapiens)

DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHL
TDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIH
INNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLK
DKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMM
NIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQ
FRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKV
TYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRK
ILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSP
LAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAA
GDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFP
AMKPE

3D structure

• PDB: 4ycu Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.
• Chain: A
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R323 E325 T330 H331 E494 N497 R553
• Catalytic site (residue number reindexed from 1): R252 E254 T259 H260 E423 N426 R482
• Enzyme Commision number: 2.7.7.-
  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	KRS	A	E325 H331 N332 F335 N497 G550 R553	E254 H260 N261 F264 N426 G479 R482	PDBbind-CN: -logKd/Ki=5.48,Kd=3.3uM BindingDB: IC50=>20000nM
BS02	LYS	A	G277 E301 E339 Y341 N497 Y499 E501 G546	G206 E230 E268 Y270 N426 Y428 E430 G475

Gene Ontology

Molecular Function

• 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

Biological Process

• GO:0006418 tRNA aminoacylation for protein translation
• GO:0006430 lysyl-tRNA aminoacylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4ycu, PDBe:4ycu, PDBj:4ycu
• PDBsum: 4ycu
• PubMed: 26074468
• UniProt: Q15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)