Structure of PDB 3a74 Chain D Binding Site BS02

Receptor Information
>3a74 Chain D (length=484) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELNDQLRVRREKLKKIEELGVDPFGKRFERTHKAEELFELYGDLSKEELE
EQQIEVAVAGRIMTKRGMGKAGFAHIQDVTGQIQIYVRQDDVGEQQYELF
KISDLGDIVGVRGTMFKTKVGELSIKVSSYEFLTKALRPLPEKDIEQRYR
QRYLDLIMNPESKKTFITRSLIIQSMRRYLDSHGYLEVETPMMHAVAGGA
AARPFITHHNALDMTLYMRIAIELHLKRLIVGGLEKVYEIGRVFRNEGIS
TRHNPEFTMLELYEAYADFRDIMKLTENLIAHIATEVLGTTKIQYGEHLV
DLTPEWRRLHMVDAIKEYVGVDFWRQMSDEEARELAKEHGVEVAPHMTFG
HIVNEFFEQKVEDKLIQPTFIYGHPVEISPLAKKNPDDPRFTDRFELFIV
GREHANAFTELNDPIDQRQRFEEQLKEREQGNDEAHEMDEDFLEALEYGM
PPTGGLGIGVDRLVMLLTNSPSIRDVLLFPQMRH
Ligand information
Ligand IDLYN
InChIInChI=1S/C6H15N3O/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H2,9,10)/p+1/t5-/m0/s1
InChIKeyHKXLAGBDJVHRQG-YFKPBYRVSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)N)N
ACDLabs 10.04O=C(N)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)N)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(N)=O
CACTVS 3.341N[CH](CCCC[NH3+])C(N)=O
FormulaC6 H16 N3 O
Name2,6-DIAMINO-HEXANOIC ACID AMIDE
ChEMBL
DrugBankDB03988
ZINC
PDB chain3a74 Chain D Residue 495 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3a74 Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for Recognition of Discriminator Base of tRNA^Lys
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G207 A208 E231 E269 Y271 N414 F416 E418
Binding residue
(residue number reindexed from 1)		G199 A200 E223 E261 Y263 N406 F408 E410
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) R253 E255 R260 H261 E411 N414 R470
Catalytic site (residue number reindexed from 1) R245 E247 R252 H253 E403 N406 R462
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:0016740 transferase activity
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:3a74, PDBe:3a74, PDBj:3a74
PDBsum3a74
PubMed
UniProtQ9RHV9|SYK_GEOSE Lysine--tRNA ligase (Gene Name=lysS)

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