Structure of PDB 8wnf Chain A Binding Site BS01

Receptor Information
>8wnf 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 IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain8wnf Chain A Residue 1006 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8wnf Structural basis for substrate and antibiotic recognition by Helicobacter pylori isoleucyl-tRNA synthetase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		C895 C898 C910 C913
Binding residue
(residue number reindexed from 1)		C893 C896 C908 C911
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8wnf, PDBe:8wnf, PDBj:8wnf
PDBsum8wnf
PubMed38246751
UniProtP56456|SYI_HELPY Isoleucine--tRNA ligase (Gene Name=ileS)

[Back to BioLiP]