Structure of PDB 6yrw Chain C Binding Site BS01

Receptor Information
>6yrw Chain C (length=410) Species: 1308 (Streptococcus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYKAFDPELWNAIDAEAERQQNNIELIASENVVSKAVMAAQGTLLTNKSA
EGYPGKRYYGGTAVIDVVETLAIERAKKLFGAKFANVQPHSGSQANAAVY
MSLIQPGDTVMGMDLSAGGHLTHGAPVSFSGKTYNFVSYNVDKESELLDY
DAILAQAKEVRPKLIVAGASAYSRIIDFAKFREIADAVGAYLMVDMAHIA
GLVASGHHPSPVPYAHVTTTTTHKTLRGPRGGLILTDDEDIAKKLNSAVF
PGLQGGPLEHVIAAKAVALKEALDPAFKEYGENVIKNAAAMADVFNQHPD
FRVISGGTNNHLFLVDVTKVVENGKVAQNVLEEVNITLNKNSIPYEQLSP
FKTSGIRVGSPAITSRGMGEAESRQIAEWMVEALENHDKPEVLERIRGDV
KVLTDAFPLY
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 chain6yrw Chain C Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6yrw Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus
Resolution2.5 Å
Binding residue
(original residue number in PDB)		S97 G98 S99 H126 D201 A203 K230
Binding residue
(residue number reindexed from 1)		S91 G92 S93 H120 D195 A197 K224
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S55 E57 D201 T227 K230 R236
Catalytic site (residue number reindexed from 1) S49 E51 D195 T221 K224 R230
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
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:6yrw, PDBe:6yrw, PDBj:6yrw
PDBsum6yrw
PubMed
UniProtQ5M0B4|GLYA_STRT1 Serine hydroxymethyltransferase (Gene Name=glyA)

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