Structure of PDB 6qvg Chain A

Receptor sequence
>6qvgA (length=453) Species: 9606 (Homo sapiens) [Search protein sequence]
WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCL
NNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYS
GSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFES
MPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCD
EVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFY
RKGVKIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYS
LQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLE
LVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEG
VNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF
DEH
3D structure
PDB6qvg Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs.
ChainA
Resolution2.32 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) Y96 E98 D251 T277 K280 R286
Catalytic site (residue number reindexed from 1) Y54 E56 D209 T235 K238 R244
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 GLY A Y141 S287 H328 A331 Y99 S245 H277 A280
BS02 DDF A L166 G170 H171 L172 S226 L124 G128 H129 L130 S184
BS03 PLP A S142 G143 S144 H171 D251 A253 H279 K280 S100 G101 S102 H129 D209 A211 H237 K238
BS04 PLP A Y96 G325 G326 Y54 G274 G275
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
View graph for
Cellular Component
External links
PDB RCSB:6qvg, PDBe:6qvg, PDBj:6qvg
PDBsum6qvg
PubMed31127856
UniProtP34897|GLYM_HUMAN Serine hydroxymethyltransferase, mitochondrial (Gene Name=SHMT2)

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