Structure of PDB 8gkt Chain B

Receptor sequence
>8gktB (length=456) Species: 9606 (Homo sapiens) [Search protein sequence]
WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFR
EYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAER
VLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFI
DEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPM
PGFDEH
3D structure
PDB8gkt Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2.
ChainB
Resolution2.64 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)		 Binding affinity
BS01 PLG B Y96 G325 Y54 G277
BS02 Y7L B E98 Y105 E56 Y63
BS03 PLG B S76 S142 G143 S144 H171 T225 S226 D251 A253 H254 T277 H279 K280 R425 S34 S100 G101 S102 H129 T183 S184 D209 A211 H212 T235 H237 K238 R377
BS04 Y7L B L166 G169 G170 H171 L172 Y176 K181 S226 L124 G127 G128 H129 L130 Y134 K139 S184
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:8gkt, PDBe:8gkt, PDBj:8gkt
PDBsum8gkt
PubMed38324671
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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