Structure of PDB 1qu3 Chain A Binding Site BS02

Receptor Information
>1qu3 Chain A (length=880) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYEKTLLMPKTDFPMRGGLPNKEPQIQEKWDAEDQYHKALEKNKGNETFI
LHDGPPYANGNLHMGHALNKILKDFIVRYKTMQGFYAPYVPGWDTHGLPI
EQALTKKGVDRKKMSTAEFREKCKEFALEQIELQKKDFRRLGVRGDFNDP
YITLKPEYEAAQIRIFGEMADKGLIYKGKKPVYWSPSSESSLAEAEIEYH
DKRSASIYVAFNVKDDKGVVDADAKFIIWTTTPWTIPSNVAITVHPELKY
GQYNVNGEKYIIAEALSDAVAEALDWDKASIKLEKEYTGKELEWVVAQHP
FLDRESLVINGDHVTTDAGTGCVHTAPGHGEDDYIVGQQYELPVISPIDD
KGVFTEEGGQFEGMFYDKANKAVTDLLTEKGALLKLDFITHSYPHDWRTK
KPVIFRATPQWFASISKVRQDILDAIENTNFKVNWGKTRIYNMVRDRGEW
VISRQRVWGVPLPVFYAENGEIIMTKETVNHVADLFAEHGSNIWFEREAK
DLLPEGFTHPGSPNGTFTKETDIMDVWFDSGSSHRGVLETRPELSFPADM
YLEGSDQYRGWFNSSITTSVATRGVSPYKFLLSHGFVMDGEGKKMSKSLG
NVIVPDQVVKQKGADIARLWVSSTDYLADVRISDEILKQTSDDYRKIRNT
LRFMLGNINDFNPDTDSIPESELLEVDRYLLNRLREFTASTINNYENFDY
LNIYQEVQNFINVELSNFYLDYGKDILYIEQRDSHIRRSMQTVLYQILVD
MTKLLAPILVHTAEEVWSHTPHVKEESVHLADMPKVVEVDQALLDKWRTF
MNLRDDVNRALETARNEKVIGKSLEAKVTIASNDKFNASEFLTSFDALHQ
LFIVSQVKVVDKLDDQATAYEHGDIVIEHA
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 chain1qu3 Chain A Residue 993 [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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PDB1qu3 Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		H64 G66 H67 E554 Q558 W562 H585 F587 V588 K595 S597 K598
Binding residue
(residue number reindexed from 1)		H63 G65 H66 E553 Q557 W561 H584 F586 V587 K594 S596 K597
Annotation score1
Binding affinityBindingDB: IC50=20000nM
Enzymatic activity
Catalytic site (original residue number in PDB) S186 S189 D397 T400 W528 K595 K598
Catalytic site (residue number reindexed from 1) S185 S188 D396 T399 W527 K594 K597
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
View graph for
Cellular Component
External links
PDB RCSB:1qu3, PDBe:1qu3, PDBj:1qu3
PDBsum1qu3
PubMed10446055
UniProtP41972|SYI1_STAAU Isoleucine--tRNA ligase (Gene Name=ileS)

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