Structure of PDB 5on3 Chain D Binding Site BS03

Receptor Information
>5on3 Chain D (length=850) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHM
GHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPW
TYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVY
KKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAYAD
ELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRP
DAFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTEKKGVDTGFKAV
HPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFASKYGLNIKPVI
LAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIADKLTAMGVGE
RKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQLPVILPEDVVM
DGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYYARYTCPQYKE
GMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRDAGMVNSDEPA
KQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGRIVKAKDAAGH
ELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFASPADMTLEWQE
SGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKALRRDVHKTIA
KVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALMQEALLAVVRM
LNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDSTLVVVQVNGKV
RAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYVPGKLLNLVVG
Ligand information
Ligand ID9YN
InChIInChI=1S/C16H25N7O4/c1-7(2)3-8(17)15(26)22-10-12(25)9(4-24)27-16(10)23-6-21-11-13(18)19-5-20-14(11)23/h5-10,12,16,24-25H,3-4,17H2,1-2H3,(H,22,26)(H2,18,19,20)/t8-,9+,10+,12+,16+/m0/s1
InChIKeyNMAIYRCXMINABF-GBPQWNHNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)C[C@@H](C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)CO)O)N
OpenEye OEToolkits 2.0.6CC(C)CC(C(=O)NC1C(C(OC1n2cnc3c2ncnc3N)CO)O)N
CACTVS 3.385CC(C)C[C@H](N)C(=O)N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n2cnc3c(N)ncnc23
CACTVS 3.385CC(C)C[CH](N)C(=O)N[CH]1[CH](O)[CH](CO)O[CH]1n2cnc3c(N)ncnc23
FormulaC16 H25 N7 O4
Name(2~{S})-~{N}-[(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-2-azanyl-4-methyl-pentanamide
ChEMBL
DrugBank
ZINC
PDB chain5on3 Chain D Residue 902 [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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PDB5on3 Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		T248 R249 V326 L327 Y330 V335
Binding residue
(residue number reindexed from 1)		T248 R249 V316 L317 Y320 V325
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) F493 H533 F543 K619 K622
Catalytic site (residue number reindexed from 1) F483 H523 F533 K609 K612
Enzyme Commision number 6.1.1.4: leucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004823 leucine-tRNA ligase activity
GO:0005515 protein binding
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006429 leucyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
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:5on3, PDBe:5on3, PDBj:5on3
PDBsum5on3
PubMed29111343
UniProtP07813|SYL_ECOLI Leucine--tRNA ligase (Gene Name=leuS)

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