Structure of PDB 5fxd Chain B Binding Site BS01

Receptor Information
>5fxd Chain B (length=525) Species: 101510 (Rhodococcus jostii RHA1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRTLPPGVSDERFDAALQRFRDVVGDKWVLSTADELEAFRDPYPVGAAEA
NLPSAVVSPESTEQVQDIVRIANEYGIPLSPVSTGKNNGYGGAAPRLSGS
VIVKTGERMNRILEVNEKYGYALLEPGVTYFDLYEYLQSHDSGLMLDCPD
LGWGSVVGNTLDRGVGYTPYGDHFMWQTGLEVVLPQGEVMRTGMGALPGS
DAWQLFPYGFGPFPDGMFTQSNLGIVTKMGIALMQRPPASQSFLITFDKE
EDLEQIVDIMLPLRINMAPLQNVPVLRNIFMDAAAVSKRTEWFDGDGPMP
AEAIERMKKDLDLGFWNFYGTLYGPPPLIEMYYGMIKEAFGKIPGARFFT
HEERDDRGGHVLQDRHKINNGIPSLDELQLLDWVPNGGHIGFSPVSAPDG
REAMKQFEMVRNRANEYNKDYAAQFIIGLREMHHVCLFIYDTAIPEAREE
ILQMTKVLVREAAEAGYGEYRTHNALMDDVMATFNWGDGALLKFHEKIKD
ALDPNGIIAPGKSGIWSQRFRGQNL
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 chain5fxd Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5fxd Biocatalytic Properties and Structural Analysis of Eugenol Oxidase from Rhodococcus Jostii Rha1: A Versatile Oxidative Biocatalyst.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		P82 V83 S84 T85 G86 K87 N88 N89 P150 D151 L152 G155 G159 N160 L162 G165 V166 Y168 I226 V227 H390 R472
Binding residue
(residue number reindexed from 1)		P81 V82 S83 T84 G85 K86 N87 N88 P149 D150 L151 G154 G158 N159 L161 G164 V165 Y167 I225 V226 H389 R471
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y91 D151 D163 D173 D283 D365 E378 L382 H390 H434 Y471 R472 K513
Catalytic site (residue number reindexed from 1) Y90 D150 D162 D172 D282 D364 E377 L381 H389 H433 Y470 R471 K512
Enzyme Commision number 1.1.3.38: vanillyl-alcohol oxidase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0004458 D-lactate dehydrogenase (cytochrome) activity
GO:0008720 D-lactate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0018465 vanillyl-alcohol oxidase activity
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:1903457 lactate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5fxd, PDBe:5fxd, PDBj:5fxd
PDBsum5fxd
PubMed27123962
UniProtQ0SBK1

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