Structure of PDB 1dfo Chain A Binding Site BS04

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 IDFFO
InChIInChI=1S/C20H23N7O7/c21-20-25-16-15(18(32)26-20)27(9-28)12(8-23-16)7-22-11-3-1-10(2-4-11)17(31)24-13(19(33)34)5-6-14(29)30/h1-4,9,12-13,22H,5-8H2,(H,24,31)(H,29,30)(H,33,34)(H4,21,23,25,26,32)/t12-,13-/m0/s1
InChIKeyVVIAGPKUTFNRDU-STQMWFEESA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC1=NC2=C(N(C=O)[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)CN2)C(=O)N1
OpenEye OEToolkits 1.7.2c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C=O)C(=O)NC(=N3)N
ACDLabs 12.01O=C(O)C(NC(=O)c1ccc(cc1)NCC2N(C=O)C=3C(=O)NC(=NC=3NC2)N)CCC(=O)O
CACTVS 3.370NC1=NC2=C(N(C=O)[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)CN2)C(=O)N1
FormulaC20 H23 N7 O7
NameN-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid;
[6S]-5-FORMYL-TETRAHYDROFOLATE;
6S-FOLINIC ACID
ChEMBLCHEMBL1908841
DrugBankDB11596
ZINCZINC000009212427
PDB chain1dfo Chain B Residue 2002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		E57 Y64 Y65
Binding residue
(residue number reindexed from 1)		E56 Y63 Y64
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
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

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

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