Structure of PDB 1y9d Chain B Binding Site BS03

Receptor Information
>1y9d Chain B (length=572) Species: 1590 (Lactiplantibacillus plantarum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRH
EEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALI
GQFGTTGMQEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGV
AVVQIPVDLPWQQIPAEDWYQTPLLPEPDVQAVTRLTQTLLAAERPLIYY
GIGARKAGKELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRAAQKP
ANEALAQADVVLFVGNNYPAFKNTRYFLQIDIDPAKLGKRHKTDIAVLAD
AQKTLAAILAQVSERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQ
VLRAVNKIAEPDAIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVG
IPGAIAAKLNYPERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNC
QYGFIKDEQEDTNQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDV
FEQAKAIAQHEPVLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYE
AQDLQPLSTYLKQFGLDDLQHQ
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 chain1y9d Chain B Residue 2703 [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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PDB1y9d The role of Val-265 for Flavin Adenine Dinulceotide (FAD) binding in pyruvate oxidase: FTIR, kinetic and crystallographic studies on the enzyme variant V265A
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G220 I221 G222 T244 P246 G284 N285 D306 I307 K311 D325 A326
Binding residue
(residue number reindexed from 1)		G201 I202 G203 T225 P227 G265 N266 D281 I282 K286 D300 A301
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) I32 G34 G35 S36 I37 E59 S82 Q122 E123 V170 R264 V394 A420 M422 D447 N474 Q476 Y477 F479 I480 E483 G546
Catalytic site (residue number reindexed from 1) I24 G26 G27 S28 I29 E51 S74 Q109 E110 V157 R245 V369 A395 M397 D422 N449 Q451 Y452 F454 I455 E458 G521
Enzyme Commision number 1.2.3.3: pyruvate oxidase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0016491 oxidoreductase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
GO:0047112 pyruvate oxidase activity

View graph for
Molecular Function
External links
PDB RCSB:1y9d, PDBe:1y9d, PDBj:1y9d
PDBsum1y9d
PubMed15794646
UniProtP37063|POXB_LACPL Pyruvate oxidase (Gene Name=pox5)

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