Structure of PDB 6smr Chain A

Receptor sequence
>6smrA (length=473) Species: 3702 (Arabidopsis thaliana) [Search protein sequence]
SNAMEPVSSWGNTSLVSVDPEIHDLIEKEKRRQCRGIELIASENFTSFAV
IEALGSALTNKYSEGIPGNRYYGGNEFIDEIENLCRSRALEAFHCDPAAW
GVNVQPYSGSPANFAAYTALLQPHDRIMGLDLPSGGHLTHGYYTSGGKKI
SATSIYFESLPYKVNFTTGYIDYDKLEEKALDFRPKLLICGGSAYPRDWD
YARFRAIADKVGALLLCDMAHISGLVAAQEAANPFEYCDVVTTTTHKSLR
GPRAGMIFYRKGPKPPKKGQPEGAVYDFEDKINFAVFPALQGGPHNHQIG
ALAVALKQANTPGFKVYAKQVKANAVALGNYLMSKGYQIVTNGTENHLVL
WDLRPLGLTGNKVEKLCDLCSITLNKNAVFGDSSALAPGGVRIGAPAMTS
RGLVEKDFEQIGEFLSRAVTLTLDIQKTYGKLLKDFNKGLVNNKDLDQLK
ADVEKFSASYEMPGFLMSEMKYK
3D structure
PDB6smr Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.
ChainA
Resolution2.12 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) Y59 E61 D215 T241 K244 R250
Catalytic site (residue number reindexed from 1) Y62 E64 D218 T244 K247 R253
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 A S39 S105 G106 S107 H134 G189 S190 D215 A217 H218 H243 K244 R389 S42 S108 G109 S110 H137 G192 S193 D218 A220 H221 H246 K247 R392
BS02 MTX A Y139 T141 S142 G143 A382 L383 Y142 T144 S145 G146 A385 L386 MOAD: Ki=179.3uM
BS03 PLS A Y59 E61 Y69 G289 Y62 E64 Y72 G292
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:1901149 salicylic acid binding
Biological Process
GO:0006730 one-carbon metabolic process
GO:0007623 circadian rhythm
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009506 plasmodesma

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6smr, PDBe:6smr, PDBj:6smr
PDBsum6smr
PubMed31873125
UniProtO23254|GLYC4_ARATH Serine hydroxymethyltransferase 4 (Gene Name=SHM4)

[Back to BioLiP]