Structure of PDB 8gky Chain A

Receptor sequence

>8gkyA (length=459) Species: 9606 (Homo sapiens) [Search protein sequence]

WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRFYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKVKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTP
MFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGAR
AERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVV
DFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARA
FPMPGFDEH

3D structure

PDB

8gky Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.

Chain

Resolution

2.77 Å

3D
structure

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Enzymatic activity

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)
BS01	ZVR	A	L166 G169 G170 H171 L172 I183 S226	L124 G127 G128 H129 L130 I141 S184
BS02	GLY	A	S76 H171 S226 R425	S34 H129 S184 R380
BS03	PLP	A	S142 G143 S144 H171 T225 S226 D251 A253 H254 H279 K280	S100 G101 S102 H129 T183 S184 D209 A211 H212 H237 K238
BS04	ZVR	A	E98 F105 Y106 F317 F320	E56 F63 Y64 F272 F275
BS05	GLY	A	E98 Y106	E56 Y64
BS06	PLP	A	Y96 G325 G326	Y54 G280 G281

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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
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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