Structure of PDB 3e9i Chain D Binding Site BS02

Receptor Information
>3e9i 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 IDXAH
InChIInChI=1S/C16H27N8O8P/c17-4-2-1-3-8(18)15(27)23-32-33(28,29)30-5-9-11(25)12(26)16(31-9)24-7-22-10-13(19)20-6-21-14(10)24/h6-9,11-12,16,25-26H,1-5,17-18H2,(H,23,27)(H,28,29)(H2,19,20,21)/t8-,9+,11+,12+,16+/m0/s1
InChIKeyUZJSLDPAROCUBS-LEJQEAHTSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(ONC(=O)C(N)CCCCN)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)ONC(=O)[C@H](CCCCN)N)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)ONC(=O)C(CCCCN)N)O)O)N
CACTVS 3.341NCCCC[CH](N)C(=O)NO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341NCCCC[C@H](N)C(=O)NO[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
FormulaC16 H27 N8 O8 P
Name5'-O-{(R)-hydroxy[(L-lysylamino)oxy]phosphoryl}adenosine
ChEMBL
DrugBank
ZINCZINC000058650767
PDB chain3e9i Chain D Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3e9i Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G207 E231 R253 H261 N262 F265 E269 E411 H412 N414 F416 E418 G465 G467 R470
Binding residue
(residue number reindexed from 1)		G199 E223 R245 H253 N254 F257 E261 E403 H404 N406 F408 E410 G457 G459 R462
Annotation score3
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:3e9i, PDBe:3e9i, PDBj:3e9i
PDBsum3e9i
PubMed19174549
UniProtQ9RHV9|SYK_GEOSE Lysine--tRNA ligase (Gene Name=lysS)

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