Structure of PDB 4ot8 Chain A Binding Site BS01

Receptor Information
>4ot8 Chain A (length=414) Species: 216591 (Burkholderia cenocepacia J2315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDRAQSTIANVDPEIFAAIEQENRRQEDHIELIASENYTSPAVMAAQGSQ
LTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRVKQLFGAEAANVQPNSGSQ
ANQGVFFAMLKPGDTIMGMSLAHGGHLTHGSPVNMSGKWFNVVSYGLNEN
EDIDYDAAEKLANEHKPKLIVAGASAFALKIDFERLAKIAKSVGAYLMVD
MAHYAGLIAAGVYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEYEKPIN
SAIFPGIQGGPLMHVIAAKAVAFKEALSPEFKEYQQKVVENARVLAETLV
KRGLRIVSGRTESHVMLVDLRAKHITGKAAEAALGAAHITVNKNAIPNDP
EKPFVTSGIRLGSPAMTTRGFGPAEAEQVGNLIADVLENPEDAATIERVR
AQVAELTKRFPVYR
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 chain4ot8 Chain A Residue 501 [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]
PDB4ot8 X-ray Crystal Structure of Serine Hydroxymethyl Transferase from Burkholderia cenocepacia bound to PLP and Serine
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S98 G99 S100 H127 D201 A203 H204 K230
Binding residue
(residue number reindexed from 1)		S97 G98 S99 H126 D200 A202 H203 K229
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y56 E58 D201 T227 K230 R236
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:0004372 glycine hydroxymethyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0050897 cobalt ion binding
GO:0070905 serine binding
Biological Process
GO:0006545 glycine 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
GO:0046655 folic acid metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ot8, PDBe:4ot8, PDBj:4ot8
PDBsum4ot8
PubMed
UniProtB4ECY9

[Back to BioLiP]