Structure of PDB 6smw Chain B Binding Site BS03

Receptor Information
>6smw Chain B (length=475) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRSSWIKQLNASLDEIDPEVADIIELEKARQWKGFELIPSENFTSLSVMQ
AVGSVMTNKYSEGYPGARYYGGNEYIDMAETLCQKRALEAFQLDPSKWGV
NVQSLSGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTKKISAV
SIFFETMPYRLDENTGYIDYDQLEKSAVLFRPKLIVAGASAYARLYDYAR
IRKVCNKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKSLRGPR
GAMIFFRKGLKEINKQGKEVMYDYEDRINQAVFPGLQGGPHNHTITGLAV
ALKQARTPEYKAYQDQVLRNCSKFAETLLAKGYDLVSGGTDNHLVLVNLK
NKGIDGSRVEKVLELVHIAANKNTVPGDVSAMVPGGIRMGTPALTSRGFI
EEDFAKVAEYFDLAVKIALKIKAESQGTKLKDFVATMQSNEKLQSEMSKL
REMVEEYAKQFPTIGFEKETMRYKE
Ligand information
Ligand IDPLS
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-/m0/s1
InChIKeyODVKKQWXKRZJLG-VIFPVBQESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CO)C(=O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
ACDLabs 10.04O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CO
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CO)C(O)=O)c1O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CO)C(O)=O)c1O
FormulaC11 H17 N2 O8 P
Name[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE;
PYRIDOXYL-SERINE-5-MONOPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000002047254
PDB chain6smw Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6smw Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
Resolution1.54 Å
Binding residue
(original residue number in PDB)		S82 S148 G149 S150 H177 A231 S232 D257 A259 H260 H285 K286 R430
Binding residue
(residue number reindexed from 1)		S40 S106 G107 S108 H135 A189 S190 D215 A217 H218 H243 K244 R388
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y102 E104 D257 T283 K286 R292
Catalytic site (residue number reindexed from 1) Y60 E62 D215 T241 K244 R250
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
Biological Process
GO:0006544 glycine metabolic process
GO:0006563 L-serine metabolic process
GO:0006730 one-carbon metabolic process
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
Cellular Component
GO:0005739 mitochondrion
GO:0009536 plastid

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6smw, PDBe:6smw, PDBj:6smw
PDBsum6smw
PubMed31873125
UniProtQ94C74|GLYM2_ARATH Serine hydroxymethyltransferase 2, mitochondrial (Gene Name=SHM2)

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