Structure of PDB 3ss9 Chain X Binding Site BS01

Receptor Information
>3ss9 Chain X (length=431) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYPLVKDLVALKETTWFNPGTTSLAEGLPYVGLTEQDVQDAHARLSRFAP
YLAKAFPETAATGGIIESELVAIPAMQKRLEKEYQQPISGQLLLKKDSHL
PISGSIKARGGIYEVLAHAEKLALEAGLLTLDDDYSKLLSPEFKQFFSQY
SIAVGSTGNLGLSIGIMSARIGFKVTVHMSADARAWKKAKLRSHGVTVVE
YEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKAQFAQ
QGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPC
MLLGVHTGLHDQISVQDIGIDNLTAADGLAVGRASGFVGRAMERLLDGFY
TLSDQTMYDMLGWLAQEEGIRLEPSALAGMAGPQRVCASVSYQQMHGFSA
EQLRNTTHLVWATGGGMVPEEEMNQYLAKGR
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 chain3ss9 Chain X Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ss9 Crystal structure of D-serine dehydratase from Escherichia coli.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		I117 K118 N170 G279 V280 G281 G283 P284 L340 T424
Binding residue
(residue number reindexed from 1)		I106 K107 N159 G268 V269 G270 G272 P273 L329 T413
Annotation score1
Enzymatic activity
Enzyme Commision number 4.3.1.18: D-serine ammonia-lyase.
Gene Ontology
Molecular Function
GO:0008721 D-serine ammonia-lyase activity
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006974 DNA damage response
GO:0009097 isoleucine biosynthetic process
GO:0036088 D-serine catabolic process
GO:0046416 D-amino acid metabolic process
GO:0051410 detoxification of nitrogen compound
GO:0070178 D-serine metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ss9, PDBe:3ss9, PDBj:3ss9
PDBsum3ss9
PubMed22197591
UniProtP00926|SDHD_ECOLI D-serine dehydratase (Gene Name=dsdA)

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