Structure of PDB 6m5w Chain A Binding Site BS01

Receptor Information
>6m5w Chain A (length=470) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFASRA
VLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQC
WGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKI
SATSIFFESMPYKVNPDTGYINYDQLEENARLFHPKLIIAGTSCYSRNLE
YARLRKIADENGAYLMADMAHISGLVAAGVVPSPFEHCHVVTTTTHKTLR
GCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIA
GVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNHLIL
VDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTS
RGLLEKDFQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAA
VQALREEVESFASLFPLPGL
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain6m5w Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6m5w Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		S119 G120 S121 H148 T202 S203 D228 K257
Binding residue
(residue number reindexed from 1)		S109 G110 S111 H138 T192 S193 D218 K247
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y73 E75 D228 T254 K257 R263
Catalytic site (residue number reindexed from 1) Y63 E65 D218 T244 K247 R253
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016832 aldehyde-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0036094 small molecule binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0048027 mRNA 5'-UTR binding
GO:0070905 serine binding
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006544 glycine metabolic process
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0009113 purine nucleobase biosynthetic process
GO:0017148 negative regulation of translation
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
GO:0045329 carnitine biosynthetic process
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
GO:0051289 protein homotetramerization
GO:1904482 cellular response to tetrahydrofolate
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6m5w, PDBe:6m5w, PDBj:6m5w
PDBsum6m5w
PubMed33521601
UniProtP34896|GLYC_HUMAN Serine hydroxymethyltransferase, cytosolic (Gene Name=SHMT1)

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