Structure of PDB 4ex5 Chain B Binding Site BS01

Receptor Information
>4ex5 Chain B (length=486) Species: 271848 (Burkholderia thailandensis E264) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DENQIVAERRDKLRALRDQGIAYPNDFQPTHHAADLQTAYADADKEALEA
KSLEVAIAGRMMLKRVMGKASFATVQDGSGQIQFFVTPADVGAETYDAFK
KWDLGDIVAARGVLFRTNKGELSVKCTQLRLLAKALRPLPDQETRYRQRY
VDLIVTPETRTTFRARTKAIASIRKFMGDADFMEVETPMLHPIPGGAAAK
PFVTHHNALDMEMFLRIAPELYLKRLIVGGFERVFEINRNFRNEGVSPRH
NPEFTMMEFYAAYTDYRWLMDFTERLIRQAAVDALGTATIQYQGRELDLA
QPFHRLTITQAIQKYAPSYTDGQLSDDAFLRSELKRLGVDVTQPAFLNAG
IGALQLALFEETAEAQLWEPTFIIDYPIEVSPLARESDTVAGITERFELF
ITGREIANGFSELNDPEDQAARFKKQVEQKDAGDEEAMFFDADYIRALEY
GMPPTGGCGIGIDRLVMLLTDSPTIRDVLLFPHLRR
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 chain4ex5 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ex5 Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		E240 E278 Y280 F430 E432 G477 G479
Binding residue
(residue number reindexed from 1)		E220 E258 Y260 F410 E412 G457 G459
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R262 E264 R269 H270 E425 N428 R484
Catalytic site (residue number reindexed from 1) R242 E244 R249 H250 E405 N408 R464
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ex5, PDBe:4ex5, PDBj:4ex5
PDBsum4ex5
PubMed28303005
UniProtQ2SXD6|SYK_BURTA Lysine--tRNA ligase (Gene Name=lysS)

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