Structure of PDB 3wqd Chain B Binding Site BS02

Receptor Information
>3wqd Chain B (length=389) Species: 518882 (Delftia sp. HT23) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHHHAMSMQDTLLTLDTPAAVIDLDRMQRNIARMQQRMDAQGVRLRPH
VKTSKSVPVAAAQRAAGASGITVSTLKEAEQFFAAGTTDILYAVSMAPHR
LPQALQLRRRGCDLKLIVDSVAAAQAIAAFGREQGEAFEVWIEIDTDGHR
SGVGADDTPLLLAIGRTLHDGGMRLGGVLTHAGSSYELDTPEALQALAER
ERAGCVQAAEALRAAGLPCPVVSVGSTPTALAASRLDGVTEVRAGVYVFF
DLVMRNIGVCAAEDVALSVLATVIGHQADKGWAIVDAGWMAMSRDRGTAR
QKQDFGYGQVCDLQGRVMPGFVLTGANQEHGILARADGAAEADIATRFPL
GTRLRILPNHACATGAQFPAYQALAADGSVQTWERLHGW
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain3wqd Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wqd Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate
Resolution1.5 Å
Binding residue
(original residue number in PDB)		H41 K43 R141 H172 Y177 S217 T218 R234 A235 G236 V237
Binding residue
(residue number reindexed from 1)		H50 K52 R150 H181 Y186 S226 T227 R243 A244 G245 V246
Annotation score1
Enzymatic activity
Enzyme Commision number 4.3.1.27: threo-3-hydroxy-D-aspartate ammonia-lyase.
Gene Ontology
Molecular Function
GO:0008721 D-serine ammonia-lyase activity
GO:0016829 lyase activity
GO:0016841 ammonia-lyase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0036088 D-serine catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3wqd, PDBe:3wqd, PDBj:3wqd
PDBsum3wqd
PubMed25715785
UniProtB2DFG5|DTHAD_DELSH D-threo-3-hydroxyaspartate dehydratase (Gene Name=dthadh)

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