Structure of PDB 6cd1 Chain B Binding Site BS01

Receptor Information
>6cd1 Chain B (length=451) Species: 3880 (Medicago truncatula) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDYGLSEADPDVHAIINKEKDRQFRSLELIASENFTSKAVMEAVGSCLTN
KYSEGLPGKRYYGGNEHIDELEILCQQRALAAFHLDGDKWGVNVQPLSGS
PANFAVYTAILKPHDRIMGLDLPHGGHLSHGFMTAKRRVSGTSIYFESMP
YRLDESTGVIDYDMLEKTAALFRPKLIIAGASAYPRDIDYARFRKIADSV
GAFLMMDMAHVSGLIAASVLADPFEFVDIVTTTTHKSLRGPRGGMIFFKK
DAVHGVDLESAINNAVFPGLQGGPHNHTIGGLAVCLKYAQSPDFKNYQNQ
VVANCRALANRLVEHEYKLVSGGSDNHLVLVDLRPSGIDGARVEKILDMA
SITLNKNSVPGDKSALVPGGIRIGSPAMTTRGLGEKEFELIADLIHEGVR
ISLEAKSLVSGTKVQDFLNFVLAPEFPLGDKVSNLRRKVEALATQYPIPG
V
Ligand information
Ligand IDPLS
InChIInChI=1S/C11H17N2O8P/c1-6-10(15)8(3-13-9(4-14)11(16)17)7(2-12-6)5-21-22(18,19)20/h2,9,13-15H,3-5H2,1H3,(H,16,17)(H2,18,19,20)/t9-/m0/s1
InChIKeyODVKKQWXKRZJLG-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CO)C(=O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
ACDLabs 10.04O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CO
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CO)C(O)=O)c1O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CO)C(O)=O)c1O
FormulaC11 H17 N2 O8 P
Name[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE;
PYRIDOXYL-SERINE-5-MONOPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000002047254
PDB chain6cd1 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6cd1 Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization.
Resolution1.91 Å
Binding residue
(original residue number in PDB)		Y134 E136 Y144 G354
Binding residue
(residue number reindexed from 1)		Y52 E54 Y62 G272
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y134 E136 D289 T315 K318 R324
Catalytic site (residue number reindexed from 1) Y52 E54 D207 T233 K236 R242
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6cd1, PDBe:6cd1, PDBj:6cd1
PDBsum6cd1
PubMed29868052
UniProtG7ILW0

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