Structure of PDB 5onh Chain A Binding Site BS04

Receptor Information
>5onh Chain A (length=860) 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
DTFMGCTYLAVAAGHPLAQKAAENNPELAAFIDECRNTKVAEAEMATMEK
KGVDTGFKAVHPLTGEEIPVWAANFVLMEYGTGAVMAVPGHDQRDYEFAS
KYGLNIKPVILAADGSEPDLSQQALTEKGVLFNSGEFNGLDHEAAFNAIA
DKLTAMGVGERKVNYRLRDWGVSRQRYWGAPIPMVTLEDGTVMPTPDDQL
PVILPEDVVMDGITSPIKADPEWAKTTVNGMPALRETDTFDTFMESSWYY
ARYTCPQYKEGMLDSEAANYWLPVDIYIGGIEHAIMHLLYFRFFHKLMRD
AGMVNSDEPAKQLLCQGMVLADAFYYVGENGERNWVSPVDAIVERDEKGR
IVKAKDAAGHELVYTGMSKMSKSKNNGIDPQVMVERYGADTVRLFMMFAS
PADMTLEWQESGVEGANRFLKRVWKLVYEHTAKGDVAALNVDALTENQKA
LRRDVHKTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALM
QEALLAVVRMLNPFTPHICFTLWQELKGEGDIDNAPWPVADEKAMVEDST
LVVVQVNGKVRAKITVPVDATEEQVRERAGQEHLVAKYLDGVTVRKVIYV
PGKLLNLVVG
Ligand information
Ligand IDVRT
InChIInChI=1S/C15H23N7O4/c1-2-3-7(16)14(25)21-9-11(24)8(4-23)26-15(9)22-6-20-10-12(17)18-5-19-13(10)22/h5-9,11,15,23-24H,2-4,16H2,1H3,(H,21,25)(H2,17,18,19)/t7-,8+,9+,11+,15+/m0/s1
InChIKeyNWKNSTYARDJRIZ-IEUWZBGXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCC[CH](N)C(=O)N[CH]1[CH](O)[CH](CO)O[CH]1n2cnc3c(N)ncnc23
CACTVS 3.385CCC[C@H](N)C(=O)N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.7.6CCCC(C(=O)N[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)CO)O)N
OpenEye OEToolkits 1.7.6CCCC(C(=O)NC1C(C(OC1n2cnc3c2ncnc3N)CO)O)N
FormulaC15 H23 N7 O4
Name2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE
ChEMBL
DrugBank
ZINCZINC000033821446
PDB chain5onh Chain A 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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PDB5onh Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		T248 L327 Y330 V335 M336 R344
Binding residue
(residue number reindexed from 1)		T248 L327 Y330 V335 M336 R344
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:5onh, PDBe:5onh, PDBj:5onh
PDBsum5onh
PubMed29111343
UniProtP07813|SYL_ECOLI Leucine--tRNA ligase (Gene Name=leuS)

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