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3THS

Crystal structure of rat native liver Glycine N-methyltransferase complexed with 5-methyltetrahydrofolate pentaglutamate

Functional Information from GO Data
ChainGOidnamespacecontents
A0005542molecular_functionfolic acid binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0005977biological_processglycogen metabolic process
A0006111biological_processregulation of gluconeogenesis
A0006544biological_processglycine metabolic process
A0006555biological_processmethionine metabolic process
A0006730biological_processone-carbon metabolic process
A0008168molecular_functionmethyltransferase activity
A0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
A0016594molecular_functionglycine binding
A0016740molecular_functiontransferase activity
A0017174molecular_functionglycine N-methyltransferase activity
A0032259biological_processmethylation
A0034708cellular_componentmethyltransferase complex
A0042802molecular_functionidentical protein binding
A0046498biological_processS-adenosylhomocysteine metabolic process
A0046500biological_processS-adenosylmethionine metabolic process
A0051289biological_processprotein homotetramerization
A0098603molecular_functionselenol Se-methyltransferase activity
A0170033biological_processL-amino acid metabolic process
A0170039biological_processproteinogenic amino acid metabolic process
A1901052biological_processsarcosine metabolic process
A1904047molecular_functionS-adenosyl-L-methionine binding
B0005542molecular_functionfolic acid binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0005977biological_processglycogen metabolic process
B0006111biological_processregulation of gluconeogenesis
B0006544biological_processglycine metabolic process
B0006555biological_processmethionine metabolic process
B0006730biological_processone-carbon metabolic process
B0008168molecular_functionmethyltransferase activity
B0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
B0016594molecular_functionglycine binding
B0016740molecular_functiontransferase activity
B0017174molecular_functionglycine N-methyltransferase activity
B0032259biological_processmethylation
B0034708cellular_componentmethyltransferase complex
B0042802molecular_functionidentical protein binding
B0046498biological_processS-adenosylhomocysteine metabolic process
B0046500biological_processS-adenosylmethionine metabolic process
B0051289biological_processprotein homotetramerization
B0098603molecular_functionselenol Se-methyltransferase activity
B0170033biological_processL-amino acid metabolic process
B0170039biological_processproteinogenic amino acid metabolic process
B1901052biological_processsarcosine metabolic process
B1904047molecular_functionS-adenosyl-L-methionine binding
C0005542molecular_functionfolic acid binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0005977biological_processglycogen metabolic process
C0006111biological_processregulation of gluconeogenesis
C0006544biological_processglycine metabolic process
C0006555biological_processmethionine metabolic process
C0006730biological_processone-carbon metabolic process
C0008168molecular_functionmethyltransferase activity
C0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
C0016594molecular_functionglycine binding
C0016740molecular_functiontransferase activity
C0017174molecular_functionglycine N-methyltransferase activity
C0032259biological_processmethylation
C0034708cellular_componentmethyltransferase complex
C0042802molecular_functionidentical protein binding
C0046498biological_processS-adenosylhomocysteine metabolic process
C0046500biological_processS-adenosylmethionine metabolic process
C0051289biological_processprotein homotetramerization
C0098603molecular_functionselenol Se-methyltransferase activity
C0170033biological_processL-amino acid metabolic process
C0170039biological_processproteinogenic amino acid metabolic process
C1901052biological_processsarcosine metabolic process
C1904047molecular_functionS-adenosyl-L-methionine binding
D0005542molecular_functionfolic acid binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0005977biological_processglycogen metabolic process
D0006111biological_processregulation of gluconeogenesis
D0006544biological_processglycine metabolic process
D0006555biological_processmethionine metabolic process
D0006730biological_processone-carbon metabolic process
D0008168molecular_functionmethyltransferase activity
D0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
D0016594molecular_functionglycine binding
D0016740molecular_functiontransferase activity
D0017174molecular_functionglycine N-methyltransferase activity
D0032259biological_processmethylation
D0034708cellular_componentmethyltransferase complex
D0042802molecular_functionidentical protein binding
D0046498biological_processS-adenosylhomocysteine metabolic process
D0046500biological_processS-adenosylmethionine metabolic process
D0051289biological_processprotein homotetramerization
D0098603molecular_functionselenol Se-methyltransferase activity
D0170033biological_processL-amino acid metabolic process
D0170039biological_processproteinogenic amino acid metabolic process
D1901052biological_processsarcosine metabolic process
D1904047molecular_functionS-adenosyl-L-methionine binding
Functional Information from PDB Data
site_idAC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE BME B 400
ChainResidue
BCYS185
BILE202
BTHR203
BTHR204
DASN210
DGLY276
DALA278

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE TAM B 293
ChainResidue
BILE34
BGLY137
BHIS142
BASN191
BTYR242
AGLU15
BTYR33

site_idAC3
Number of Residues12
DetailsBINDING SITE FOR CHAIN E OF 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE
ChainResidue
ATYR5
ATHR7
BSER205
BLEU207
BTHR217
BARG239
CSER3
CVAL4
CTYR5
DLEU207
DHIS214
DMET215

site_idAC4
Number of Residues12
DetailsBINDING SITE FOR CHAIN F OF 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE
ChainResidue
ALEU207
AHIS214
AMET215
BSER3
BVAL4
BTYR5
CSER146
CHIS214
CMET215
CARG239
DTYR5
DARG6

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22037183","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3THR","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"3THS","evidenceCode":"ECO:0000312"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22037183","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3THS","evidenceCode":"ECO:0000312"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues20
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1NBI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"8810903","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1XVA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8810903","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1XVA","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1NBI","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8810903","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XVA","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues4
DetailsModified residue: {"description":"N-acetylvaline","evidences":[{"source":"PubMed","id":"2822402","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues4
DetailsModified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues16
DetailsModified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idMCSA1
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
AGLU25electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
AALA141electrostatic stabiliser, hydrogen bond acceptor
ASER146activator
ATYR179electrostatic stabiliser
ALEU198electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

site_idMCSA2
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
BGLU25electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
BALA141electrostatic stabiliser, hydrogen bond acceptor
BSER146activator
BTYR179electrostatic stabiliser
BLEU198electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

site_idMCSA3
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
CGLU25electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
CALA141electrostatic stabiliser, hydrogen bond acceptor
CSER146activator
CTYR179electrostatic stabiliser
CLEU198electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

site_idMCSA4
Number of Residues5
DetailsM-CSA 23
ChainResidueDetails
DGLU25electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
DALA141electrostatic stabiliser, hydrogen bond acceptor
DSER146activator
DTYR179electrostatic stabiliser
DLEU198electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

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PDB entries from 2025-07-23

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