Structure of PDB 3if9 Chain D Binding Site BS02

Receptor Information
>3if9 Chain D (length=361) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGML
SAHEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEE
DVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFV
CKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASG
VWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDACYIVPRKSG
RLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAGLRP
GTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQ
DWLHAFRIDRK
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain3if9 Chain D Residue 371 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3if9 Glyphosate resistance by engineering the flavoenzyme glycine oxidase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G11 G13 I14 I15 F33 E34 S35 R41 T42 T43 A46 A47 G48 M49 V174 S202 G203 G300 R302 H327 F328 R329 N330 G331 I332
Binding residue
(residue number reindexed from 1)		G11 G13 I14 I15 F33 E34 S35 R41 T42 T43 A46 A47 G48 M49 V171 S199 G200 G297 R299 H324 F325 R326 N327 G328 I329
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) A47 G48 M49
Catalytic site (residue number reindexed from 1) A47 G48 M49
Enzyme Commision number 1.4.3.19: glycine oxidase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0043799 glycine oxidase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0009228 thiamine biosynthetic process
GO:0009229 thiamine diphosphate biosynthetic process
GO:0009635 response to herbicide
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3if9, PDBe:3if9, PDBj:3if9
PDBsum3if9
PubMed19864430
UniProtO31616|GLYOX_BACSU Glycine oxidase (Gene Name=thiO)

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