Structure of PDB 3zgz Chain A Binding Site BS02

Receptor Information
>3zgz Chain A (length=860) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQEQYRPEEIESKVQLHWDEKRTFEVTEDESKEKYYCLSMLPYPSGRLHM
GHVRNYTIGDVIARYQRMLGKNVLQPIGWDAFGLPAEGAAVKNNTAPAPW
TYDNIAYMKNQLKMLGFGYDWSRELATCTPEYYRWEQKFFTELYKKGLVY
KKTSAVNWCPNDQTVLANEQVIDGCCWRCDTKVERKEIPQWFIKITAYAD
ELLNDLDKLDHWPDTVKTMQRNWIGRSEGVEITFNVNDYDNTLTVYTTRP
DTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEK
KGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFAS
KYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIA
DKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQL
PVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYY
ARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRD
AGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGR
IVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFAS
PADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKA
LRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALM
QEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDST
LVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYV
PGKLLNLVVG
Ligand information
Ligand ID84T
InChIInChI=1S/C16H25N6O8P/c1-7(2)11(24)12(25)15(26)21-31(27,28)29-4-8-3-9(23)16(30-8)22-6-20-10-13(17)18-5-19-14(10)22/h5-9,11-12,16,23-25H,3-4H2,1-2H3,(H2,17,18,19)(H2,21,26,27,28)/t8-,9-,11+,12-,16+/m0/s1
InChIKeyKHSKVNAFZAVNFC-UVIICUSPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC(C)[C@H]([C@@H](C(=O)NP(=O)(O)OC[C@@H]1C[C@@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)O
CACTVS 3.385CC(C)[C@@H](O)[C@H](O)C(=O)N[P](O)(=O)OC[C@@H]1C[C@H](O)[C@@H](O1)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.9.2CC(C)C(C(C(=O)NP(=O)(O)OCC1CC(C(O1)n2cnc3c2ncnc3N)O)O)O
CACTVS 3.385CC(C)[CH](O)[CH](O)C(=O)N[P](O)(=O)OC[CH]1C[CH](O)[CH](O1)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3)C(O)C(O)C(C)C
FormulaC16 H25 N6 O8 P
Name[(2S,4S,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-N-[(2S,3R)-4-methyl-2,3-bis(oxidanyl)pentanoyl]phosphonamidic acid
ChEMBL
DrugBank
ZINCZINC000098208590
PDB chain3zgz Chain A Residue 1862 [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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PDB3zgz Plant Tumour Biocontrol Agent Employs a tRNA-Dependent Mechanism to Inhibit Leucyl-tRNA Synthetase
Resolution2.4 Å
Binding residue
(original residue number in PDB)		M40 L41 P42 Y43 H49 G51 H52 N55 D80 S496 G530 E532 H533 H537 Q566 M568 V569 M620 K622
Binding residue
(residue number reindexed from 1)		M40 L41 P42 Y43 H49 G51 H52 N55 D80 S496 G530 E532 H533 H537 Q566 M568 V569 M620 K622
Annotation score2
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) L41 H49 H52 D80 C159 D162 C176 C179 F493 H533 F543 K619 K622
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
View graph for
Cellular Component
External links
PDB RCSB:3zgz, PDBe:3zgz, PDBj:3zgz
PDBsum3zgz
PubMed23361008
UniProtP07813|SYL_ECOLI Leucine--tRNA ligase (Gene Name=leuS)

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