Structure of PDB 8bap Chain L Binding Site BS01

Receptor Information
>8bap Chain L (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
NLPSAVVSPESTEQVQDIVRIANEYGIPLHPVSTGKNNGYGGAAPRLSGS
VIVKTGERMNRILEVNEKYGYALLEPGVTYFDLYEYLQSHDSGLMLDCPD
LGWGSVVGNTLDRGVGYTPYGDHFMWQTGLEVVLPQGEVMRTGMGALPGS
DAWQLFPYGFGPFPDGMFTQSNLGIVTKMGIALMQRPPASQSFLITFDKE
EDLEQIVDIMLPLRINMAPLQNVPVLRNIFMDAAAVSKRTEWFDGDGPMP
AEAIERMKKDLDLGFWNFYGTLYGPPPLIEMYYGMIKEAFGKIPGARFFT
HEERDDRGGHVLQDRHKINNGIPSLDELQQLDWVPNGGHIGFVPVSAPDG
REAMKQFEMVRNRANEYNKDYMAQFVIGLREMYHVCLFIYDTADPEAREE
ILQMTKVLVREAAEAGYGEYRTHNALMDDVMATFNWGDGALLKFHEKIKD
ALDPNGIIAPGKSGIWPQRFRGQNL
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 chain8bap Chain L 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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PDB8bap One-pot biocatalytic synthesis of rac-syringaresinol from a lignin-derived phenol
Resolution2.3 Å
Binding residue
(original residue number in PDB)		P82 V83 S84 T85 G86 K87 N88 N89 P150 D151 S156 G159 N160 L162 G165 V166 Y168 V227 E378 H390 R472 K513
Binding residue
(residue number reindexed from 1)		P81 V82 S83 T84 G85 K86 N87 N88 P149 D150 S155 G158 N159 L161 G164 V165 Y167 V226 E377 H389 R471 K512
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:8bap, PDBe:8bap, PDBj:8bap
PDBsum8bap
PubMed38026814
UniProtQ0SBK1

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