Structure of PDB 1ryi Chain D Binding Site BS01

Receptor Information
>1ryi Chain D (length=364) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGML
GAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAF
SEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEP
YFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVV
ASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPR
KSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAG
LRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKE
VNQDWLHAFRIDRK
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 chain1ryi Chain D Residue 9400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ryi Structure-function correlation in glycine oxidase from Bacillus subtilis
Resolution1.8 Å
Binding residue
(original residue number in PDB)		I10 G11 G13 I15 E34 S35 R41 T42 T43 A46 A47 G48 M49 V174 S202 W205 F209 G300 R302 H327 R329 N330 G331 I332
Binding residue
(residue number reindexed from 1)		I10 G11 G13 I15 E34 S35 R41 T42 T43 A46 A47 G48 M49 V174 S202 W205 F209 G300 R302 H327 R329 N330 G331 I332
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:1ryi, PDBe:1ryi, PDBj:1ryi
PDBsum1ryi
PubMed15105420
UniProtO31616|GLYOX_BACSU Glycine oxidase (Gene Name=thiO)

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