Structure of PDB 6smw Chain D Binding Site BS04

Receptor Information
>6smw Chain D (length=480) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNAEKSRSSWIKQLNASLDEIDPEVADIIELEKARQWKGFELIPSENFTS
LSVMQAVGSVMTNKYSEGYPGARYYGGNEYIDMAETLCQKRALEAFQLDP
SKWGVNVQSLSGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTK
KISAVSIFFETMPYRLDENTGYIDYDQLEKSAVLFRPKLIVAGASAYARL
YDYARIRKVCNKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKS
LRGPRGAMIFFRKGLKEINKQGKEVMYDYEDRINQAVFPGLQGGPHNHTI
TGLAVALKQARTPEYKAYQDQVLRNCSKFAETLLAKGYDLVSGGTDNHLV
LVNLKNKGIDGSRVEKVLELVHIAANKNTVPGDVSAMVPGGIRMGTPALT
SRGFIEEDFAKVAEYFDLAVKIALKIKAESQGTKLKDFVATMQSNEKLQS
EMSKLREMVEEYAKQFPTIGFEKETMRYKE
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 chain6smw Chain D Residue 1310 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		S148 G149 S150 H177 D257 A259 H285 K286
Binding residue
(residue number reindexed from 1)		S111 G112 S113 H140 D220 A222 H248 K249
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y102 E104 D257 T283 K286 R292
Catalytic site (residue number reindexed from 1) Y65 E67 D220 T246 K249 R255
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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