Structure of PDB 5yb0 Chain D Binding Site BS01

Receptor Information
>5yb0 Chain D (length=345) Species: 5759 (Entamoeba histolytica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IHNFGAGPAAMAKEVIEATAKAVNNFWEGLSILEISHRSKEWINVMNETK
ALMKEVMDIPEGYEILFFGGGASLQFLMVAMNLLNKKACYLDTGVWASKA
IKEAENIGEVKIIGTSKDKNYTYIPEYQIPSDYDYFHITTNNTIYGTEIR
KDIESPIPLVADMSSDILSKPIDISKYSLIYAGAQKNCGAAGVTIVIIKK
EILGKVQRKIPIILDYQVHILNNSMYNTPPVISIFTVNQTLKYIKKIGGL
KKIQELNEEKARLLYAEIDRNKIFRGTVRKKDRSIMNVCFVYKQLENEFS
EYALQKGIIGIKGHRSVGGFRASIYNAVTIESVQALIKCMHDFEQ
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 chain5yb0 Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yb0 N-terminal residues are crucial for quaternary structure and active site conformation for the phosphoserine aminotransferase from enteric human parasite E. histolytica.
Resolution2.94 Å
Binding residue
(original residue number in PDB)		G76 A77 S78 W101 D167 S169 Q190 K191
Binding residue
(residue number reindexed from 1)		G71 A72 S73 W96 D162 S164 Q185 K186
Annotation score1
Enzymatic activity
Enzyme Commision number 2.6.1.52: phosphoserine transaminase.
Gene Ontology
Molecular Function
GO:0004648 O-phospho-L-serine:2-oxoglutarate aminotransferase activity
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006563 L-serine metabolic process
GO:0006564 L-serine biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yb0, PDBe:5yb0, PDBj:5yb0
PDBsum5yb0
PubMed30959130
UniProtQ60I38

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