Structure of PDB 6ymd Chain A

Receptor sequence
>6ymdA (length=420) Species: 72020 (Aphanothece halophytica) [Search protein sequence]
QTNLDFLLQTDPTISGMMQKELQRQREHLELIASENFTSPAVMATQGSVL
TNKYAEGLPKKRYYGGCEFIDEIEQVAIDRAKELFGAASANVQPHSGAQA
NFAVFLTLLKPGDKIMGMDLSHGGHLTHGSPANVSGKWFEAVHYGVSQET
EQLDYDHILEVARQERPKLIICGYSAYPRIINFEKFRAIADEVGAYLLAD
IAHIAGLVASGHHPNPVPHCDVVTTTTHKTLRGPRGGLILTRDPELGKKF
NKSVFPGTQGGPLEHVIAGKAVAFGEALKPEFKAYSGQVIANAQAMAQQL
QNRGFKIVSGGTDNHLMLVDLRSVNLTGKQADQLVSDVNITANKNTVPFD
PESPFVTSGLRLGSPAMTTRGLGTEDFAEIANIIADRLQNPEDEQVKQAC
VQRVAALCERFPLYPHLNAP
3D structure
PDB6ymd Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.
ChainA
Resolution1.25 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) Y56 E58 D202 T228 K231 R237
Catalytic site (residue number reindexed from 1) Y54 E56 D200 T226 K229 R235
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 PMP A S98 G99 A100 H127 Y176 S177 D202 A204 T228 K231 S96 G97 A98 H125 Y174 S175 D200 A202 T226 K229
BS02 MLI A Y56 E58 Y66 Y54 E56 Y64
BS03 MLI A S36 H127 H205 K231 R363 S34 H125 H203 K229 R361
BS04 PMP A Y56 G263 Y54 G261
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
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:0032259 methylation
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:6ymd, PDBe:6ymd, PDBj:6ymd
PDBsum6ymd
PubMed32417544
UniProtI7H6W6

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