Structure of PDB 8c9g Chain B Binding Site BS02

Receptor Information
>8c9g Chain B (length=921) Species: 1404 (Priestia megaterium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEYKDTLLMPKTEFPMRGNLPNREPKMQEQWAEMNIYEKVQKRTEGRPLF
VLHDGPPYANGDIHMGHALNKILKDFIVRYKSMSGFCAPYVPGWDTHGLP
IETALTKNKKVNRKEMTVAEFRKLCEQYAWEQVNGQREQFKRLGVRGDWD
NPYVTLQPQYEAQQIKVFGDMAKKGYIYKGLKPVYWSPSSESALAEAEIE
YYDKRSASIYVAFNVKDGKGVLEQDEKFIIWTTTPWTMPANQGIAVNPEL
QYSVVEADGAKYVVATELIETVAKEIEWADYKTLRTVKGSELERVVAEHP
IYKRDSLVVLGDHVTTDAGTGCVHTAPGHGEDDFIVGQKYGLEVLCPVDS
KGHMTNEAPGFEGLFYDKANKPITDKLEEEGALLKLSFITHSYPHDWRTK
KPTIFRATAQWFASIKDFREDLLKAVEKTKWVPTWGETRLYNMVRDRGDW
CISRQRAWGVPIPVFYAENEEPIITDETIEHVSNLFREHGSNVWFEREAK
DLLPEGFTHEGSPNGRFTKETDIMDVWFDSGSSHQAVLEEREDLQRPADL
YLEGSDQYRGWFNSSLSTSVAVTGEAPYKGVLSHGFALDGEGRKMSKSLG
NVVIPEKVMKQLGADILRLWVASVDYQADVRVSDNILKQVAEVYRKIRNT
FRFLLGNLADFNPTTDAVAVEDLREVDRYMLVKLNKLIDKVKKSYDSYEF
SSIYHAVHNFCTIDMSSFYLDFAKDVLYIEAENNVERRSIQTVLYETLLS
LTKLVSPILSHTADEVWVHIPNVTEESVQLVDMPEVQEIEGADQLVEKWD
AFMELRDEVLKALEQARNEKVIGKSLEAKLTLYPTADTKELLASISENVG
QLFIVSDLEVAEGEAPAEAQKFSYASIVVSKAEGEKCERCWVVSPTVGED
QDHPTLCTRCADVVKNHYVQQ
Ligand information
Ligand IDMRC
InChIInChI=1S/C26H44O9/c1-16(13-23(30)33-11-9-7-5-4-6-8-10-22(28)29)12-20-25(32)24(31)19(15-34-20)14-21-26(35-21)17(2)18(3)27/h13,17-21,24-27,31-32H,4-12,14-15H2,1-3H3,(H,28,29)/b16-13+/t17-,18-,19-,20-,21-,24+,25-,26-/m0/s1
InChIKeyMINDHVHHQZYEEK-HBBNESRFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C1C(O1)CC2COC(C(C2O)O)CC(=CC(=O)OCCCCCCCCC(=O)O)C)C(C)O
CACTVS 3.385C[CH](O)[CH](C)[CH]1O[CH]1C[CH]2CO[CH](CC(C)=CC(=O)OCCCCCCCCC(O)=O)[CH](O)[CH]2O
CACTVS 3.385C[C@H](O)[C@H](C)[C@@H]1O[C@H]1C[C@H]2CO[C@@H](C/C(C)=C/C(=O)OCCCCCCCCC(O)=O)[C@H](O)[C@@H]2O
OpenEye OEToolkits 2.0.7C[C@H]([C@H]1[C@@H](O1)C[C@H]2CO[C@H]([C@@H]([C@@H]2O)O)C/C(=C/C(=O)OCCCCCCCCC(=O)O)/C)[C@H](C)O
FormulaC26 H44 O9
NameMUPIROCIN;
9-[(E)-4-[(2S,3R,4R,5S)-3,4-bis(oxidanyl)-5-[[(2S,3S)-3-[(2S,3S)-3-oxidanylbutan-2-yl]oxiran-2-yl]methyl]oxan-2-yl]-3-methyl-but-2-enoyl]oxynonanoic acid;
PSEUDOMONIC ACID
ChEMBLCHEMBL719
DrugBankDB00410
ZINCZINC000004102194
PDB chain8c9g Chain B Residue 1002 [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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PDB8c9g Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif
Resolution2.8 Å
Binding residue
(original residue number in PDB)		P56 P57 H64 G66 N70 E553 G554 D556 Q557 W561 F586 A587 M595 S596 K597
Binding residue
(residue number reindexed from 1)		P56 P57 H64 G66 N70 E553 G554 D556 Q557 W561 F586 A587 M595 S596 K597
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:8c9g, PDBe:8c9g, PDBj:8c9g
PDBsum8c9g
PubMed37679387
UniProtA0A0B6A6A8

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