Structure of PDB 4dpg Chain F Binding Site BS01

Receptor Information
>4dpg Chain F (length=505) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDH
LTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFI
HINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGL
KDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPM
MNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGR
QFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYK
VTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETR
KILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMS
PLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKA
AGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLF
PAMKP
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain4dpg Chain F Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dpg Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription.
Resolution2.844 Å
Binding residue
(original residue number in PDB)		G277 E301 E339 Y341 N497 Y499 E501 G546
Binding residue
(residue number reindexed from 1)		G207 E231 E269 Y271 N427 Y429 E431 G476
Annotation score5
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.
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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