Structure of PDB 6m5w Chain A

Receptor sequence
>6m5wA (length=470) Species: 9606 (Homo sapiens) [Search protein sequence]
DADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFASRA
VLEALGSCLNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQC
WGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKI
SATSIFFESMPYKVNPDTGYINYDQLEENARLFHPKLIIAGTSCYSRNLE
YARLRKIADENGAYLMADMAHISGLVAAGVVPSPFEHCHVVTTTTHKTLR
GCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIA
GVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNHLIL
VDLRSKGTDGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTS
RGLLEKDFQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQAA
VQALREEVESFASLFPLPGL
3D structure
PDB6m5w Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate.
ChainA
Resolution3.1 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
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 PLP A S119 G120 S121 H148 T202 S203 D228 K257 S109 G110 S111 H138 T192 S193 D218 K247
BS02 DXC A Y82 Y83 Y72 Y73
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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