Structure of PDB 6ti4 Chain A Binding Site BS03

Receptor Information
>6ti4 Chain A (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 IDO3Z
InChIInChI=1S/C11H17N2O8P/c1-6-10(15)8(3-13-9(4-14)11(16)17)7(2-12-6)5-21-22(18,19)20/h2,9,13-15H,3-5H2,1H3,(H,16,17)(H2,18,19,20)/t9-/m1/s1
InChIKeyODVKKQWXKRZJLG-SECBINFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CO)C(O)=O)c1O
OpenEye OEToolkits 2.0.7Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CO)C(=O)O)O
OpenEye OEToolkits 2.0.7Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CO)C(=O)O)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CO)C(O)=O)c1O
FormulaC11 H17 N2 O8 P
Name(2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain6ti4 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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PDB6ti4 Crystal Structure of Y55S Serine Hydroxymethyltransferase variant from Streptococcus thermophilus in complex with gem-diamine intermediate of D-serine
Resolution1.93 Å
Binding residue
(original residue number in PDB)		E57 Y65 G261
Binding residue
(residue number reindexed from 1)		E51 Y59 G255
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:6ti4, PDBe:6ti4, PDBj:6ti4
PDBsum6ti4
PubMed
UniProtQ5M4W1|GLYA_STRT2 Serine hydroxymethyltransferase (Gene Name=glyA)

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