Structure of PDB 4udp Chain B Binding Site BS01

Receptor Information
>4udp Chain B (length=512) Species: 887061 (Methylovorus sp. MP688) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IFDYVIVGGGTAGSVLANRLSARPENRVLLIEAGIDTPENNIPPEIHDGL
RPWLPRLSGDKFFWPNLTIHRAAREPQFYEQGRLLGGGSSVNMVVSNRGL
PRDYDEWQALGADGWDWQGVLPYFIKTERDADYGDDPLHGNAGPIPIGRV
DSRHWSDFTVAATQALEAAGLPNIHDQNARFDDGYFPPAFTLKGEERFSA
ARGYLDASVRVRPNLSLWTESRVLKLLTTGNAITGVSVLRGRETLQVQAR
EVILTAGALQSPAILLRTGIGPAADLHALGIPVLADRPGVGRNLWEHSSI
GVVAPLTEQARADARHQLGIRASSGVDPATPSDLFLHIGADPVSGLASAV
FWVNKPSSTGWLKLKDADPFSYPDVDFNLLSDPRDLGRLKAGLRLITHYF
AAPSLAKYGLALALSRFAAPQPGGPLLNDLLQDEAALERYLRTNVGGVWH
ASGTARIGRADDSQAVVDKAGRVYGVTGLRVADASIMPTVPTANTNLPTL
MLAEKIADAILT
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 chain4udp Chain B Residue 700 [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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PDB4udp Structure-Based Enzyme Tailoring of 5-Hydroxymethylfurfural Oxidase
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G12 G14 T15 A16 E36 A37 W68 G92 G97 G98 N102 M103 V105 V233 T265 A266 G267 W466 D500 A501 N511 T512 N513
Binding residue
(residue number reindexed from 1)		G8 G10 T11 A12 E32 A33 W64 G82 G87 G88 N92 M93 V95 V223 T255 A256 G257 W449 D483 A484 N494 T495 N496
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) L335 F368 W369 V465 H467 A510 N511
Catalytic site (residue number reindexed from 1) L318 F351 W352 V448 H450 A493 N494
Enzyme Commision number 1.1.3.47: 5-(hydroxymethyl)furfural oxidase.
1.8.3.-
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0016670 oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor
GO:0016899 oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding

View graph for
Molecular Function
External links
PDB RCSB:4udp, PDBe:4udp, PDBj:4udp
PDBsum4udp
PubMed
UniProtE4QP00|HMFO_METS6 5-(hydroxymethyl)furfural oxidase (Gene Name=MPQ_0130)

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