Structure of PDB 3td7 Chain A Binding Site BS01

Receptor Information
>3td7 Chain A (length=253) Species: 212035 (Acanthamoeba polyphaga mimivirus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HNGLITKIWGTAGWTFNHAVTFGYPLNPTSDDKRRYKNYFISLGDVLPCR
LCRESYKKFITTGKTALTNEVLRNRHTLTKWFYDVHNAVNNKLEVDYGLS
YEDVVNKYESFRAKCGKVTPLDHKAFSFKKLYYMDAPIVSLDKVENFVRI
ARMRGISDKYFAFLELATVLNGDFNELKKQSSWEYRNKYAQKKIRHMREN
AIPSIEEQGYWKGTPTIDELKLLLFLASNLNRTEVNDAINNVERLESTHY
IEN
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 chain3td7 Chain A Residue 334 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3td7 Exploring ORFan domains in giant viruses: structure of mimivirus sulfhydryl oxidase R596.
Resolution2.21 Å
Binding residue
(original residue number in PDB)		T37 G41 T42 G44 W45 H49 C83 Y114 H117 N118 V120 K123 L124 Y128 L130 V135 D174 R237
Binding residue
(residue number reindexed from 1)		T6 G10 T11 G13 W14 H18 C52 Y83 H86 N87 V89 K92 L93 Y97 L99 V104 D135 R198
Annotation score1
Enzymatic activity
Enzyme Commision number 1.8.3.2: thiol oxidase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016971 flavin-dependent sulfhydryl oxidase activity
GO:0016972 thiol oxidase activity
GO:0050660 flavin adenine dinucleotide binding
Cellular Component
GO:0044423 virion component

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3td7, PDBe:3td7, PDBj:3td7
PDBsum3td7
PubMed23209798
UniProtQ5UP54|YR596_MIMIV Probable FAD-linked sulfhydryl oxidase R596 (Gene Name=MIMI_R596)

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