Structure of PDB 6ymf Chain A Binding Site BS01

Receptor Information
>6ymf Chain A (length=418) Species: 72020 (Aphanothece halophytica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTNLDFLLQTDPTISGMMQKELQRQREHLELIASENFTSPAVMATQGSVL
TNKYAEGLPKKRYYGGCEFIDEIEQVAIDRAKELFGAASANVQPHSGAQA
NFAVFLTLLKPGDKIMGMDLSHGGHLTHGSPANVSGKWFEAVHYGVSQET
EQLDYDHILEVARQERPKLIICGYSAYPRIINFEKFRAIADEVGAYLLAD
IAHIAGLVASGHHPNPVPHCDVVTTTTHKTLRGPRGGLILTRDPELGKKF
NKSVFPGTQGGPLEHVIAGKAVAFGEALKPEFKAYSGQVIANAQAMAQQL
QNRGFKIVSGGTDNHLMLVDLRSVNLTGKQADQLVSDVNITANKNTVPFD
PESPFVTSGLRLGSPAMTTRGLGTEDFAEIANIIADRLQNPEDEQVKQAC
VQRVAALCERFPLYPHLN
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 chain6ymf Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ymf Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.
Resolution1.63 Å
Binding residue
(original residue number in PDB)		S36 S98 G99 A100 H127 S177 D202 A204 H205 T228 K231 R363
Binding residue
(residue number reindexed from 1)		S34 S96 G97 A98 H125 S175 D200 A202 H203 T226 K229 R361
Annotation score1
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.
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:6ymf, PDBe:6ymf, PDBj:6ymf
PDBsum6ymf
PubMed32417544
UniProtI7H6W6

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