Structure of PDB 5mxu Chain A Binding Site BS01

Receptor Information
>5mxu Chain A (length=553) Species: 69488 (Penicillium simplicissimum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFRPLTLPPKLSLSDFNEFIQDIIRIVGSENVEVISSKIVDGSYMKPTHT
HDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLWPISIGRNSG
YGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEA
NNLRDKLWLDVPDLGGGSVLGNAVERGVGYTPYGDHWMMHSGMEVVLANG
ELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQS
NMGIVTKIGIWLMPNPRGYQSYLITLPKDGDLKQAVDIIRPLRLGMALQN
VPTIRHILLDAAVLGDKRSYSSRTEPLSDEELDKIAKQLNLGRWNFYGAL
YGPEPIRRVLWETIKDAFSAIPGVKFYFPEDTPENSVLRVRDKTMQGIPT
YDELKWIDWLPNGAHLFFSPIAKVSGEDAMMQYAVTKKRCQEAGLDFIGT
FTVGMREMHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEFRTHL
AFMDQIMETYNWNNSSFLRFNEVLKNAVDPNGIIAPGKSGVWPSQYSHVT
WKL
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 chain5mxu Chain A Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5mxu Two tyrosine residues, Tyr-108 and Tyr-503, are responsible for the deprotonation of phenolic substrates in vanillyl-alcohol oxidase.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		P99 S101 I102 G103 R104 N105 P169 D170 L171 G174 S175 N179 E182 V185 Y187 V262 W413 H422 F424 R504 K545
Binding residue
(residue number reindexed from 1)		P92 S94 I95 G96 R97 N98 P162 D163 L164 G167 S168 N172 E175 V178 Y180 V255 W406 H415 F417 R497 K538
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y108 D170 E182 D192 D317 V397 E410 I414 H422 H466 F503 R504 K545
Catalytic site (residue number reindexed from 1) Y101 D163 E175 D185 D310 V390 E403 I407 H415 H459 F496 R497 K538
Enzyme Commision number 1.1.3.38: vanillyl-alcohol oxidase.
Gene Ontology
Molecular Function
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:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0015945 methanol metabolic process
GO:1903457 lactate catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5mxu, PDBe:5mxu, PDBj:5mxu
PDBsum5mxu
PubMed28717004
UniProtP56216|VAOX_PENSI Vanillyl-alcohol oxidase (Gene Name=VAOA)

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