Structure of PDB 1y9d Chain C Binding Site BS03

Receptor Information
>1y9d Chain C (length=556) Species: 1590 (Lactiplantibacillus plantarum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNILAGAAVIKVLEAWGVDHLYGIPGGSINSIMDALSAERDRIHYIQVRH
EEVGAMAAAADAKLTGKIGVCFGSAGPGGTHLMNGLYDAREDHVPVLALI
GQFGTTGEMNENPIYADVADYNVTAVNAATLPHVIDEAIRRAYAHQGVAV
VQIPVDLPWQQIPAELPEPDVQAVTRLTQTLLAAERPLIYYGIGARKAGK
ELEQLSKTLKIPLMSTYPAKGIVADRYPAYLGSANRAAQKPANEALAQAD
VVLFVGNNYKNTRYFLQIDIDPAKLGKRHKTDIAVLADAQKTLAAILAQV
SERESTPWWQANLANVKNWRAYLASLEDKQEGPLQAYQVLRAVNKIAEPD
AIYSIDVGDINLNANRHLKLTPSNRHITSNLFATMGVGIPGAIAAKLNYP
ERQVFNLAGDGGASMTMQDLATQVQYHLPVINVVFTNCQYGFIKDEQEDT
NQNDFIGVEFNDIDFSKIADGVHMQAFRVNKIEQLPDVFEQAKAIAQHEP
VLIDAVITGDRPLPAEKLRLDSAMSSAADIEAFKQRYEAQDLQPLSTYLK
QFGLDD
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain1y9d Chain C Residue 2802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		D396 M422 G446 D447 G448 N474 Q476 Y477 G478 F479 I480
Binding residue
(residue number reindexed from 1)		D359 M385 G409 D410 G411 N437 Q439 Y440 G441 F442 I443
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) I32 G34 G35 S36 I37 E59 S82 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 E108 V155 R236 V357 A383 M385 D410 N437 Q439 Y440 F442 I443 E446 G509
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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