Structure of PDB 8gky Chain B Binding Site BS03

Receptor Information

>8gky Chain B (length=461) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRFYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKADPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQAC
TPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDG
ARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRR
VVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFA
RAFPMPGFDEH

Ligand information

Ligand ID

PLP

InChI

InChI=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)

InChIKey

NGVDGCNFYWLIFO-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0	Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04	O=P(O)(O)OCc1cnc(c(O)c1C=O)C

Formula

C8 H10 N O6 P

Name

PYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate

PDB chain

8gky Chain A Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8gky Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
Resolution	2.77 Å
Binding residue (original residue number in PDB)	Y96 G325
Binding residue (residue number reindexed from 1)	Y54 G282
Annotation score	1

Enzymatic activity

Enzyme Commision number

2.1.2.1: glycine hydroxymethyltransferase.

Gene Ontology

	Molecular Function
GO:0003682	chromatin binding
GO:0004372	glycine hydroxymethyltransferase activity
GO:0005515	protein binding
GO:0008732	L-allo-threonine aldolase activity
GO:0016597	amino acid binding
GO:0016740	transferase activity
GO:0030170	pyridoxal phosphate binding
GO:0042802	identical protein binding

	Biological Process
GO:0002082	regulation of oxidative phosphorylation
GO:0006544	glycine metabolic process
GO:0006545	glycine biosynthetic process
GO:0006563	L-serine metabolic process
GO:0006564	L-serine biosynthetic process
GO:0006730	one-carbon metabolic process
GO:0008284	positive regulation of cell population proliferation
GO:0019264	glycine biosynthetic process from serine
GO:0034340	response to type I interferon
GO:0035999	tetrahydrofolate interconversion
GO:0046653	tetrahydrofolate metabolic process
GO:0051262	protein tetramerization
GO:0051289	protein homotetramerization
GO:0070129	regulation of mitochondrial translation
GO:0070536	protein K63-linked deubiquitination
GO:1903715	regulation of aerobic respiration

	Cellular Component
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005739	mitochondrion
GO:0005743	mitochondrial inner membrane
GO:0005759	mitochondrial matrix
GO:0015630	microtubule cytoskeleton
GO:0042645	mitochondrial nucleoid
GO:0070062	extracellular exosome
GO:0070552	BRISC complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:8gky, PDBe:8gky, PDBj:8gky
PDBsum	8gky
PubMed	38324671
UniProt	P34897\|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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