Structure of PDB 8wo2 Chain A Binding Site BS02

Receptor Information
>8wo2 Chain A (length=918) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EYKDTLNLNTTTFSMKGNLSVNEPKTYAKWQEQQAFKRMQARKDNHGDFT
LHDGPPYANGHLHLGHALNKILKDIVVKREYFKGKKIYYTPGWDCHGLPI
EQQILERLEKEKTSLENPTLFREKCRDHAKKFLEIQKNEFLQLGVLGDFE
DPYKTMDFKFEASIYRALVEVAKKGLLKERHKPIYWSYACESALAEAEVE
YKMKKSPSIFVAFGLKKESLEKLKVKKASLVIWTTTPWTLYANVAIALKK
DAVYALTQKGYLVAKALHEKLAALGVVDNEITHEFNSNDLEYLVATNPLN
QRDSLVALGEHVGLEDGTGAVHTAPGHGEEDYYLGLRYNLEVLMSVDEKG
CYDEGIIHNQLLDESYLGEHVFKAQKRIIEQLGDSLLLEQEIEHSYPHCW
RTHKPVIYRATTQWFILMDEPFIQNDGSQKTLREVALDAIEKVEFVPSSG
KNRLKTMIENRPDWCLSRQRKWGVPLAFFIDKRTNKPCFESEVLEHVANL
FEKKGCDVWWEYSVKDLLPPSYQEDAKHYEKIMHILDVWFDSGSTFKAVL
EDYHGEKGQSPSDVILEGSDQHRGWFQSSLLIGCVLNNQAPFKKVITHGF
IVDEKGEKMSKSKGNVVSLDKLLKTHGSDVVRLWVAFNDYQNDLRVSQTF
FTQTEQHYKKFRNTLKFLLANFSDMDLKNLERPHNFSPLDHFMLETLETI
SAGVNSAFEEHDFVKGLNILMAFVTNELSGIYLDACKDSLYCDSKNNEKR
QAIQMVLLATASKLCYFLAPILTHTIEEVLEHSQALRIFLQAKDVFDLKD
ISVSEKLHLKEFKKPENFEAVLALRSAFNEELDRLKKEGVIKNSLECAIE
VKEKALDENLVEELLMVSFVGIAKEKLSETPAFTLFKAPFYKCPRCWRFK
SELENTPCKRCEQVLKER
Ligand information
Ligand IDWN9
InChIInChI=1S/C15H23N6O8P/c1-6(2)8(16)15(24)29-30(25,26)27-3-7-10(22)11(23)14(28-7)21-5-20-9-12(17)18-4-19-13(9)21/h4-8,10-11,14,22-23H,3,16H2,1-2H3,(H,25,26)(H2,17,18,19)/t7-,8+,10-,11-,14-/m1/s1
InChIKeyKAVINRUMCQFLGF-NIXGFCADSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)C(C(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.385CC(C)[CH](N)C(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.385CC(C)[C@H](N)C(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.7CC(C)[C@@H](C(=O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
FormulaC15 H23 N6 O8 P
Name[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-3-methyl-butanoate;
Valyl adenylate
ChEMBL
DrugBank
ZINC
PDB chain8wo2 Chain A Residue 1003 [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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PDB8wo2 Structural basis for substrate and antibiotic recognition by Helicobacter pylori isoleucyl-tRNA synthetase.
Resolution2.34 Å
Binding residue
(original residue number in PDB)
P57 Y59 H65 G67 D96 W541 E569 G570 D572 Q573 W577 H600 F602 I603
Binding residue
(residue number reindexed from 1)
P55 Y57 H63 G65 D94 W539 E567 G568 D570 Q571 W575 H598 F600 I601
Annotation score3
Enzymatic activity
Enzyme Commision number 6.1.1.5: isoleucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004822 isoleucine-tRNA ligase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006428 isoleucyl-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:8wo2, PDBe:8wo2, PDBj:8wo2
PDBsum8wo2
PubMed38246751
UniProtP56456|SYI_HELPY Isoleucine--tRNA ligase (Gene Name=ileS)

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