Structure of PDB 6ild Chain B

Receptor sequence

>6ildB (length=499) Species: 9606 (Homo sapiens)

DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHL
TDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIH
INNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLDKETR
YRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPG
GAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEG
IDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPD
GPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDI
CVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWH
RSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEA
MFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKP

3D structure

• PDB: 6ild Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex.
• Chain: B
• Resolution: 1.882 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R323 E325 T330 H331 E494 N497 R553
• Catalytic site (residue number reindexed from 1): R247 E249 T254 H255 E418 N421 R477
• 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	LYS	B	G277 E301 E339 Y341 Y499 E501 G546 W547	G201 E225 E263 Y265 Y423 E425 G470 W471
BS02	MG	B	E487 E494	E411 E418
BS03	45A	B	T330 H331 F335 E494 R553	T254 H255 F259 E418 R477

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:6ild, PDBe:6ild, PDBj:6ild
• PDBsum: 6ild
• PubMed: 30733335
• UniProt: Q15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)