Structure of PDB 1eqb Chain D Binding Site BS04

Receptor Information
>1eqb Chain D (length=417) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQ
LTNKYAEGYPGKRYFGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQ
ANFAVYTALLEPGDTVLGMNLAHGGHLTHGSPVNFSGKLYNIVPYGIDAT
GHIDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVD
MAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYK
KLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVE
VFLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVP
NDPKSPFVTSGIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIE
RIKGKVLDICARYPVYA
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 chain1eqb Chain C Residue 3293 [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]
PDB1eqb Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		E57 Y64
Binding residue
(residue number reindexed from 1)		E57 Y64
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y55 E57 D200 T226 K229 R235
Catalytic site (residue number reindexed from 1) Y55 E57 D200 T226 K229 R235
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:1eqb, PDBe:1eqb, PDBj:1eqb
PDBsum1eqb
PubMed10858298
UniProtP0A825|GLYA_ECOLI Serine hydroxymethyltransferase (Gene Name=glyA)

[Back to BioLiP]