Structure of PDB 8c9d Chain A Binding Site BS03

Receptor Information
>8c9d Chain A (length=1032) Species: 1404 (Priestia megaterium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKEVNVRESSQEREQRIQQQWQKGNVFQQSVQNREGYPSFVFYEGPPTAN
GLPHVGHALGRTIKDVVARYKTMTGHQVIRKAGWDTHGLPVELGVEKQLG
ISGKHDIEKYGVEAFINKCKESVFVYEKQQRTFTEQLGYWVDMEDPYITL
ENSYIESVWNVLGTIHDKGLLYKGHRVSPYCPSCQTSLSSHEVAQGYKDV
KDLTVTVKFKVKNRDNEYFLGWTTTPWTLPSNVALAVHEEMSYVRAEQGD
SVYIVAEALADKVLKGEYSVLSHHKGNELKGMSYEPPFNFVKVEKGHEVV
TADYVTDQSGTGVVHLAPAYGEDDYRVVKENGFSFVNVVDEKGQYTSEVP
PFQGRFVKDCDVDIVRYLANQDVLYHKEKHEHSYPFCWRCDSPLLYYANE
SWFIQTTALKEQFLKNNESVKWYPDHIKHGRFGKFLENMVDWNISRKRYW
GTPLNVWECEGCQHQVAPKSIKELQKHASHYVDDSIELHKPYVDDVQLTC
PVCSGEMKRTPEVIDVWFDSGSMPFAQYHYPFENSELFQKQFPADVIAEG
IDQTRGWFYSLMAVSTLFTGKAPYKRVLSLGHVLDENGQKMSKSKGNALD
PVDLIHTFGADALRWALLADSAPWNPKKFSERVVQEAKSKVIDTLVNVYG
FYVLYAKLDGYDPEQTYELKKTKLDEWILSRLHSTVKRATVHLEDYGFTS
AAREIAVFIEELSNWYVRRSRDRFWSEGMDGEKAAAYDTLHEVLVTLSQL
LAPFTPFVADDVHENLTGKSVHLADYPACDQTKVNEKLEKEMAAVLQVVE
LGRSIRNTHSLKVKQPLQSLSLVVTEEDVEWKAYRDVIKDELNVKNFNVE
QDDDKLVSYVLKLDFKQAGPKFGKQVNEVNQALKNLSEEKGKEFVEQGKL
SVTLASGENLTLETEDVLVEKVPKEGFAVASNGMYTAVLDTALTEELVQE
GVAREVIRAVQDYRKKLDLPVNSRINLELSGDEEVQKAVAKFETLLQENL
LLHSLSVKETIKNGETVKVGTKQVVLRVLNQS
Ligand information
Ligand IDILA
InChIInChI=1S/C16H26N8O6S/c1-3-7(2)9(17)15(27)23-31(28,29)22-4-8-11(25)12(26)16(30-8)24-6-21-10-13(18)19-5-20-14(10)24/h5-9,11-12,16,22,25-26H,3-4,17H2,1-2H3,(H,23,27)(H2,18,19,20)/t7-,8+,9-,11+,12+,16+/m0/s1
InChIKeyXVTRBLLRODNOJV-VBJYJYTRSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC[C@H](C)[C@H](N)C(=O)N[S](=O)(=O)NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)NCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)C(C)CC
OpenEye OEToolkits 1.5.0CC[C@H](C)[C@@H](C(=O)NS(=O)(=O)NC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)N
CACTVS 3.341CC[CH](C)[CH](N)C(=O)N[S](=O)(=O)NC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CCC(C)C(C(=O)NS(=O)(=O)NCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)N
FormulaC16 H26 N8 O6 S
NameN-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE
ChEMBL
DrugBankDB01755
ZINCZINC000031976783
PDB chain8c9d Chain A Residue 1103 [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]
PDB8c9d Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif
Resolution2.3 Å
Binding residue
(original residue number in PDB)		P46 P47 T48 H54 G56 H57 D85 W517 S520 E549 G550 D552 Q553 H582 V583
Binding residue
(residue number reindexed from 1)		P46 P47 T48 H54 G56 H57 D85 W517 S520 E549 G550 D552 Q553 H582 V583
Annotation score2
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8c9d, PDBe:8c9d, PDBj:8c9d
PDBsum8c9d
PubMed37679387
UniProtA0A0B6AVD3

[Back to BioLiP]