Structure of PDB 4o6z Chain B Binding Site BS01

Receptor Information
>4o6z Chain B (length=445) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPGMFNNDPLQKYDKELFDLLEKEKNRQIETINLIASENLTNTAVRECLG
DRISNKYSEGYPHKRYYGGNDYVDKIEELCYKRALEAFNVSEEEWGVNVQ
PLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDL
FESKLYKCNSEGYVDMESVRNLALSFQPKVIICGYTSYPRDIDYKGFREI
CDEVNAYLFADISHISSFVACNLLNNPFTYADVVTTTTHKILRGPRSALI
FFNKKRNPGIDQKINSSVFPSFQGGPHNNKIAAVACQLKEVNTPEFKEYT
KQVLLNSKALAECLLKRNLDLVTNGTDNHLIVVDLRKYNITGSKLQETCN
AINIALNKNTIPSDVDCVSPSGIRIGTPALTTRGCKEKDMEFIADMLLKA
ILLTDELQQKYGKKLVDFKKGLVNNPKIDELKKEVVQWAKNLPFA
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 chain4o6z Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4o6z The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities.
Resolution2.98 Å
Binding residue
(original residue number in PDB)		S100 G101 S102 H129 D208 S210 H211 H236 K237
Binding residue
(residue number reindexed from 1)		S103 G104 S105 H132 D211 S213 H214 H239 K240
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y54 E56 D208 T234 K237 R243
Catalytic site (residue number reindexed from 1) Y57 E59 D211 T237 K240 R246
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008168 methyltransferase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006730 one-carbon metabolic process
GO:0019264 glycine biosynthetic process from serine
GO:0032259 methylation
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0070178 D-serine metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0020011 apicoplast

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4o6z, PDBe:4o6z, PDBj:4o6z
PDBsum4o6z
PubMed24914963
UniProtQ8I566|GLYA_PLAF7 Serine hydroxymethyltransferase (Gene Name=SHMT)

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