Structure of PDB 2dkj Chain B Binding Site BS01

Receptor Information
>2dkj Chain B (length=402) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGY
PGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMAL
MEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEV
RRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLV
AAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGI
QGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIV
TGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTS
GIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHP
MP
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 chain2dkj Chain B Residue 510 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2dkj Crystal Structure of T.th.HB8 Serine Hydroxymethyltransferase
Resolution1.15 Å
Binding residue
(original residue number in PDB)		S93 G94 S95 H122 D197 A199 H200 T223 H225 K226
Binding residue
(residue number reindexed from 1)		S88 G89 S90 H117 D192 A194 H195 T218 H220 K221
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y51 E53 D197 T223 K226 R232
Catalytic site (residue number reindexed from 1) Y46 E48 D192 T218 K221 R227
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2dkj, PDBe:2dkj, PDBj:2dkj
PDBsum2dkj
PubMed
UniProtQ5SI56|GLYA_THET8 Serine hydroxymethyltransferase (Gene Name=glyA)

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