Structure of PDB 1dfo Chain A Binding Site BS03

Receptor Information
>1dfo Chain A (length=416) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQL
TNKYAEGYPGKRYYGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQA
NFAVYTALLEPGDTVLGMNLAHGGHLTHGSPVNFSGKLYNIVPYGIDATG
HIDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVDM
AHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYKK
LNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVEV
FLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPN
DPKSPFVTSGIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIER
IKGKVLDICARYPVYA
Ligand information
Ligand IDPLG
InChIInChI=1S/C10H15N2O7P/c1-6-10(15)8(3-11-4-9(13)14)7(2-12-6)5-19-20(16,17)18/h2,11,15H,3-5H2,1H3,(H,13,14)(H2,16,17,18)
InChIKeyFEVQWBMNLWUBTF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CNCC(O)=O)c1O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNCC(=O)O)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
FormulaC10 H15 N2 O7 P
NameN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE];
N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE
ChEMBL
DrugBankDB02824
ZINCZINC000002046831
PDB chain1dfo Chain B Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1dfo Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y55 Y65 G262
Binding residue
(residue number reindexed from 1)		Y54 Y64 G261
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y55 E57 D200 T226 K229 R235
Catalytic site (residue number reindexed from 1) Y54 E56 D199 T225 K228 R234
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008732 L-allo-threonine aldolase activity
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006545 glycine biosynthetic process
GO:0006546 glycine catabolic process
GO:0006564 L-serine biosynthetic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0008652 amino acid biosynthetic process
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1dfo, PDBe:1dfo, PDBj:1dfo
PDBsum1dfo
PubMed10656824
UniProtP0A825|GLYA_ECOLI Serine hydroxymethyltransferase (Gene Name=glyA)

[Back to BioLiP]