Structure of PDB 3a5y Chain A Binding Site BS01

Receptor Information
>3a5y Chain A (length=297) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASWQPSASIPNLLKRAAIMAEIRRFFADRGVLEVETPCMSQATVTDIHLV
PFETRFVGPGHSQGMNLWLMTSPEYHMKRLLVAGCGPVFQLCRSFRNEEM
GRYHNPEFTMLEWYRPHYDMYRLMNEVDDLLQQVLDCPAAESLSYQQAFL
RYLEIDPLSADTLLQLLFTFGVEPNIGKEKPTFVYHFPASQASLAQISTE
DHRVAERFEVYYKGIELANGFHELTDAREQQQRFEQDNRKRAARGLPQHP
IDQNLIEALKVGMPDCSGVALGVDRLVMLALGAETLAEVIAFSVDRA
Ligand information
Ligand IDKAA
InChIInChI=1S/C16H26N8O7S/c17-4-2-1-3-8(18)15(27)23-32(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)(H2,19,20,21)/t8-,9+,11+,12+,16+/m0/s1
InChIKeyNARKTLKJPPMFJF-LEJQEAHTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CCCCN)N)O)O)N
CACTVS 3.341NCCCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341NCCCC[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CCCCN
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CCCCN)N)O)O)N
FormulaC16 H26 N8 O7 S
Name5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE;
5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE
ChEMBLCHEMBL1163083
DrugBank
ZINCZINC000040956727
PDB chain3a5y Chain A Residue 1990 [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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PDB3a5y A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		S76 E78 R100 H108 N109 F112 M114 Y118 E244 L245 N247 F249 E251 G296 A298 G300 R303
Binding residue
(residue number reindexed from 1)		S72 E74 R96 H104 N105 F108 M110 Y114 E216 L217 N219 F221 E223 G268 A270 G272 R275
Annotation score2
Binding affinityMOAD: Kd=11nM
PDBbind-CN: -logKd/Ki=7.96,Kd=11nM
Enzymatic activity
Enzyme Commision number 6.3.1.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016880 acid-ammonia (or amide) ligase activity
GO:0042803 protein homodimerization activity
GO:0052868 protein-lysine lysyltransferase activity
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
GO:0043687 post-translational protein modification
GO:0071468 cellular response to acidic pH
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:3a5y, PDBe:3a5y, PDBj:3a5y
PDBsum3a5y
PubMed20729861
UniProtP0A8N7|EPMA_ECOLI Elongation factor P--(R)-beta-lysine ligase (Gene Name=epmA)

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