Structure of PDB 6ymd Chain A Binding Site BS04

Receptor Information
>6ymd Chain A (length=420) 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
VQRVAALCERFPLYPHLNAP
Ligand information
Ligand IDPMP
InChIInChI=1S/C8H13N2O5P/c1-5-8(11)7(2-9)6(3-10-5)4-15-16(12,13)14/h3,11H,2,4,9H2,1H3,(H2,12,13,14)
InChIKeyZMJGSOSNSPKHNH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CN)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN)c1O
FormulaC8 H13 N2 O5 P
Name4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE;
PYRIDOXAMINE-5'-PHOSPHATE
ChEMBLCHEMBL1235353
DrugBankDB02142
ZINCZINC000001532708
PDB chain6ymd Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ymd Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.
Resolution1.25 Å
Binding residue
(original residue number in PDB)		Y56 G263
Binding residue
(residue number reindexed from 1)		Y54 G261
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
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6ymd, PDBe:6ymd, PDBj:6ymd
PDBsum6ymd
PubMed32417544
UniProtI7H6W6

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