Structure of PDB 5on2 Chain A Binding Site BS03

Receptor Information
>5on2 Chain A (length=862) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRL
HMGHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPA
PWTYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGL
VYKKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAY
ADELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTT
RPDAFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATM
EKKGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEF
ASKYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNA
IADKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDD
QLPVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSW
YYARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLM
RDAGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEK
GRIVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMF
ASPADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQ
KALRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRA
LMQEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVED
STLVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVI
YVPGKLLNLVVG
Ligand information
Ligand IDLSS
InChIInChI=1S/C16H25N7O7S/c1-7(2)3-8(17)15(26)22-31(27,28)29-4-9-11(24)12(25)16(30-9)23-6-21-10-13(18)19-5-20-14(10)23/h5-9,11-12,16,24-25H,3-4,17H2,1-2H3,(H,22,26)(H2,18,19,20)/t8-,9+,11+,12+,16+/m0/s1
InChIKeyXFEDFDTWJLGMBO-LEJQEAHTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
OpenEye OEToolkits 1.7.6CC(C)CC(C(=O)NS(=O)(=O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
ACDLabs 12.01O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CC(C)C
CACTVS 3.370CC(C)C[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370CC(C)C[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
FormulaC16 H25 N7 O7 S
Name5'-O-(L-leucylsulfamoyl)adenosine;
5-O-N-LEUCYL-SULFAMOYLADENOSINE
ChEMBLCHEMBL1163081
DrugBank
ZINCZINC000033821383
PDB chain5on2 Chain A Residue 901 [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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PDB5on2 Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		M40 L41 P42 Y43 G51 H52 N55 D80 S496 G530 E532 H533 H537 Q566 M568 V569 M620
Binding residue
(residue number reindexed from 1)		M42 L43 P44 Y45 G53 H54 N57 D82 S498 G532 E534 H535 H539 Q568 M570 V571 M622
Annotation score2
Binding affinityBindingDB: Ki=0.139000nM
Enzymatic activity
Catalytic site (original residue number in PDB) L41 H49 H52 D80 C159 D162 C176 C179 F493 H533 F543 K619 K622
Catalytic site (residue number reindexed from 1) L43 H51 H54 D82 C161 D164 C178 C181 F495 H535 F545 K621 K624
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:5on2, PDBe:5on2, PDBj:5on2
PDBsum5on2
PubMed29111343
UniProtP07813|SYL_ECOLI Leucine--tRNA ligase (Gene Name=leuS)

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