Structure of PDB 4ysh Chain B Binding Site BS03

Receptor Information
>4ysh Chain B (length=368) Species: 235909 (Geobacillus kaustophilus HTA426) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
THRYDVAIVGGGVIGAAIGFELAKRRHRVAIFEKGTMGSGASSAAAGMLG
AQSEFSTSSPLVPLALQSRALMPALAEELRERTGIDIGLVEKGLIKLATT
EEEADDLYRHYTFWRGIGEPVQWLTKGEALEMEPRLAEALAGAMYIPGDG
QVSAPDLAAALAYAAASAGACLYEYTEVFDIRSDSSGHVLDTTGGTFAAE
AVVIASGAWAARLGARVGLSLSVYPVKGECVMVRAPVPLLQTTVFAKNGC
YIVPKSGNRLLIGATSTPGTFDRRVSAGGVMNLLHRAAHLVPDIEQAEWV
ASWSGIRPQTEDGLPYLGEHPERRGLFVAAGHYRNGILLSPLTGLLVADL
VERKETAFDLAPFSLTRH
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 chain4ysh Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ysh Crystal structure of glycine oxidase from Geobacillus kaustophilus
Resolution2.2 Å
Binding residue
(original residue number in PDB)		V10 G11 G13 I15 F33 E34 K35 G41 A42 S43 A46 A47 M49 V180 S208 W211 R309 H334 R336 N337 G338 I339 L340
Binding residue
(residue number reindexed from 1)		V9 G10 G12 I14 F32 E33 K34 G40 A41 S42 A45 A46 M48 V178 S206 W209 R307 H332 R334 N335 G336 I337 L338
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) A46 M49 L50 Q53 I264 L285 G307 N337 L340
Catalytic site (residue number reindexed from 1) A45 M48 L49 Q52 I262 L283 G305 N335 L338
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:0051289 protein homotetramerization
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:4ysh, PDBe:4ysh, PDBj:4ysh
PDBsum4ysh
PubMed
UniProtQ5L2C2|GLYOX_GEOKA Glycine oxidase (Gene Name=thiO)

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