Structure of PDB 6smn Chain D

Receptor sequence
>6smnD (length=480) Species: 3702 (Arabidopsis thaliana) [Search protein sequence]
SNAEKSRSSWIKQLNASLDEIDPEVADIIELEKARQWKGFELIPSENFTS
LSVMQAVGSVMTNKYSEGYPGARYYGGNEYIDMAETLCQKRALEAFQLDP
SKWGVNVQSLSGSPANFQVYTALLKPHERIMALDLPHGGHLSHGYQTDTK
KISAVSIFFETMPYRLDENTGYIDYDQLEKSAVLFRPKLIVAGASAYARL
YDYARIRKVCNKQKAVMLADMAHISGLVAAGVIPSPFEYADVVTTTTHKS
LRGPRGAMIFFRKGLKEINKQGKEVMYDYEDRINQAVFPGLQGGPHNHTI
TGLAVALKQARTPEYKAYQDQVLRNCSKFAETLLAKGYDLVSGGTDNHLV
LVNLKNKGIDGSRVEKVLELVHIAANKNTVPGDVSAMVPGGIRMGTPALT
SRGFIEEDFAKVAEYFDLAVKIALKIKAESQGTKLKDFVATMQSNEKLQS
EMSKLREMVEEYAKQFPTIGFEKETMRYKE
3D structure
PDB6smn Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
ChainD
Resolution1.63 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 PLS D Y102 E104 Y112 G330 Y65 E67 Y75 G293
BS02 MTX D Y182 T184 D185 Y145 T147 D148
BS03 SER D S82 H260 X286 R430 S45 H223 X249 R393
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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Cellular Component
External links
PDB RCSB:6smn, PDBe:6smn, PDBj:6smn
PDBsum6smn
PubMed31873125
UniProtQ94C74|GLYM2_ARATH Serine hydroxymethyltransferase 2, mitochondrial (Gene Name=SHM2)

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