Structure of PDB 7ywv Chain C Binding Site BS01

Receptor Information
>7ywv Chain C (length=524) Species: 101510 (Rhodococcus jostii RHA1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RTLPPGVSDERFDAALQRFRDVVGDKWVLSTADELEAFRDPYPVGAAEAN
LPSAVVSPESTEQVQDIVRIANEYGIPLHPVSTGKNNGYGGAAPRLSGSV
IVKTGERMNRILEVNEKYGYALLEPGVTYFDLYEYLQSHDSGLMLDCPEL
GWGSVVGNTLDRGVGYTPYGDHFMWQTGLEVVLPQGEVMRTGMGALPGSD
AWQLFPYGFGPFPDGMFTQSNLGIVTKMGIALMQRPPASQSFLITFDKEE
DLEQIVDIMLPLRINMAPLQNVPVLRNIFMDAAAVSKRTEWFDGDGPMPA
EAIERMKKDLDLGFWNFYGTLYGPPPLIEMYYGMIKEAFGKIPGARFFTH
EERDDRGGHVLQDRHKINNGIPSLDELQLLDWVPNGGHIGFVPVSAPDGR
EAMKQFEMVRNRANEYNKDYMASFIIGLREMYHVCLFIYDTADPEAREEI
LQMTKVLVREAAEAGYGEYRTHNALMDDVMATFNWGDGALLKFHEKIKDA
LDPNGIIAPGKSGIWPQRFRGQNL
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 chain7ywv Chain C Residue 601 [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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PDB7ywv Structure- and computational-aided engineering of an oxidase to produce isoeugenol from a lignin-derived compound.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		P82 V83 S84 T85 G86 K87 N88 N89 P150 E151 L152 G155 S156 G159 N160 L162 G165 V166 Y168 I226 V227 H390 R472
Binding residue
(residue number reindexed from 1)		P80 V81 S82 T83 G84 K85 N86 N87 P148 E149 L150 G153 S154 G157 N158 L160 G163 V164 Y166 I224 V225 H388 R470
Annotation score1
Enzymatic activity
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:7ywv, PDBe:7ywv, PDBj:7ywv
PDBsum7ywv
PubMed36418310
UniProtQ0SBK1

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