Structure of PDB 5yb8 Chain B Binding Site BS03

Receptor Information
>5yb8 Chain B (length=549) Species: 1355242 (Pseudomonas sp. AIU 813) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKPITIFGPDFPFAFDDWLEHPAGLGSIPAARHGEEVAIVGAGIAGLVAA
YELMKLGLKPVVYEASKMGGRLRSQAFNGTDGIIAELGGMRFPVSSTAFY
HYVDKLGLETKPFPNPLTPASRSTVIDLEGQTYYAEKAADLPALFQEVTD
AWADALESGARFGDIQQAIRDRDVPRLKELWNTLVPLWDDRTFYDFVATS
KAFAKLSFQHREVFGQVGFGTGGWDSDFPNSMLEIFRVVMTNCDDHQHLV
VGGVEQVPQGIWRHVPERCAHWPEGTSLSSLHGGAPRTGVKRIARASDGR
LAVTDNWGDCRHYAAVLTTCQSWLLTTQIDCEESLFSQKMWMALDRTRYM
QSSKTFVMVDRPFWKDKDPETGRDLMSMTLTDRLTRGTYLFDNGDDKPGV
ICLSYAWMSDALKMLPHPVEKRVQLALDALKKIYPKTDIAGHIIGDPITI
SWEADPHFLGAFKGALPGHYRYNQRMYAHFMQAQMPVEQRGIFIAGDDVS
WTPAWVEGAVQTSLNAVWGIMNHFGGKTHADNPGPGDVFDEIGQIALAD
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 chain5yb8 Chain B Residue 603 [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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PDB5yb8 Ligand complex structures of l-amino acid oxidase/monooxygenase from
Resolution2.3 Å
Binding residue
(original residue number in PDB)		V51 G52 G54 I55 A56 Y74 E75 A76 G81 R82 L83 G99 G100 M101 R102 F103 G300 V301 C331 L335 I340 W463 F469 A472 F473 D508 A515 W516 V517
Binding residue
(residue number reindexed from 1)		V40 G41 G43 I44 A45 Y63 E64 A65 G70 R71 L72 G88 G89 M90 R91 F92 G289 V290 C320 L324 I329 W452 F458 A461 F462 D497 A504 W505 V506
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E245 K365
Catalytic site (residue number reindexed from 1) E234 K354
Enzyme Commision number 1.13.12.3: tryptophan 2-monooxygenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0001716 L-amino-acid oxidase activity
GO:0004497 monooxygenase activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0009063 amino acid catabolic process
GO:0009851 auxin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5yb8, PDBe:5yb8, PDBj:5yb8
PDBsum5yb8
PubMed29511608
UniProtW6JQJ6

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