Structure of PDB 2nyg Chain C Binding Site BS01

Receptor Information
>2nyg Chain C (length=270) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKKIVESTTFPRTKQSITEDLKALGLKKGMTVLVHSSLSSIGWVNGGAVA
VIQALIDVVTEEGTIVMPSQSVELSDPKEWGNPPVPEEWWDIIRESMPAY
NSNYTPTTRGMGQIVELFRSYPEVKRSNHPNYSFVAWGKHKNKILNQHPL
EFGLGEQSPLGKLYIRESYVLLLGADFDSSTCFHLAEYRIPYQKIINRGA
PIIVEGKRVWKEYKELEFREELFQEVGQAFEAEHNMKVGKVGSANCRLFS
LTEAVDFAEKWFINNDSKNI
Ligand information
Ligand IDCOA
InChIInChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
InChIKeyRGJOEKWQDUBAIZ-IBOSZNHHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
ACDLabs 10.04O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC21 H36 N7 O16 P3 S
NameCOENZYME A
ChEMBLCHEMBL1213327
DrugBankDB01992
ZINCZINC000008551087
PDB chain2nyg Chain C Residue 303 [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]
PDB2nyg Crystal structure of YokD protein from Bacillus subtilis
Resolution2.6 Å
Binding residue
(original residue number in PDB)		L2 S37 S38 L39 S40 G43 W44 V45 G48 G113 Q114 A176
Binding residue
(residue number reindexed from 1)		L1 S36 S37 L38 S39 G42 W43 V44 G47 G112 Q113 A175
Annotation score4
Enzymatic activity
Enzyme Commision number 2.3.1.-
Gene Ontology
Molecular Function
GO:0008080 N-acetyltransferase activity
GO:0016746 acyltransferase activity
Biological Process
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2nyg, PDBe:2nyg, PDBj:2nyg
PDBsum2nyg
PubMed
UniProtO32003|YOKD_BACSU SPbeta prophage-derived aminoglycoside N(3')-acetyltransferase-like protein YokD (Gene Name=yokD)

[Back to BioLiP]