Structure of PDB 4dpg Chain B

Receptor sequence
>4dpgB (length=506) Species: 9606 (Homo sapiens) [Search protein sequence]
VDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDH
LTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFI
HINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGL
KDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPM
MNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGR
QFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYK
VTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETR
KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMS
PLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKA
AGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLF
PAMKPE
3D structure
PDB4dpg Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription.
ChainB
Resolution2.844 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) R323 E325 T330 H331 E494 N497 R553
Catalytic site (residue number reindexed from 1) R253 E255 T260 H261 E424 N427 R483
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 N497 Y499 E501 G546 G207 E231 E269 Y271 N427 Y429 E431 G476
BS02 APC B R323 T330 H331 N332 F335 E494 R553 I564 R253 T260 H261 N262 F265 E424 R483 I494
BS03 MG B E487 E494 E417 E424
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4dpg, PDBe:4dpg, PDBj:4dpg
PDBsum4dpg
PubMed23159739
UniProtQ15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)

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