Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3THS

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005542	molecular_function	folic acid binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005977	biological_process	glycogen metabolic process
A	0006111	biological_process	regulation of gluconeogenesis
A	0006544	biological_process	glycine metabolic process
A	0006555	biological_process	methionine metabolic process
A	0006730	biological_process	one-carbon metabolic process
A	0008168	molecular_function	methyltransferase activity
A	0008757	molecular_function	S-adenosylmethionine-dependent methyltransferase activity
A	0016594	molecular_function	glycine binding
A	0016740	molecular_function	transferase activity
A	0017174	molecular_function	glycine N-methyltransferase activity
A	0032259	biological_process	methylation
A	0034708	cellular_component	methyltransferase complex
A	0042802	molecular_function	identical protein binding
A	0046498	biological_process	S-adenosylhomocysteine metabolic process
A	0046500	biological_process	S-adenosylmethionine metabolic process
A	0051289	biological_process	protein homotetramerization
A	0098603	molecular_function	selenol Se-methyltransferase activity
A	0170033	biological_process	L-amino acid metabolic process
A	0170039	biological_process	proteinogenic amino acid metabolic process
A	1901052	biological_process	sarcosine metabolic process
A	1904047	molecular_function	S-adenosyl-L-methionine binding
B	0005542	molecular_function	folic acid binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005977	biological_process	glycogen metabolic process
B	0006111	biological_process	regulation of gluconeogenesis
B	0006544	biological_process	glycine metabolic process
B	0006555	biological_process	methionine metabolic process
B	0006730	biological_process	one-carbon metabolic process
B	0008168	molecular_function	methyltransferase activity
B	0008757	molecular_function	S-adenosylmethionine-dependent methyltransferase activity
B	0016594	molecular_function	glycine binding
B	0016740	molecular_function	transferase activity
B	0017174	molecular_function	glycine N-methyltransferase activity
B	0032259	biological_process	methylation
B	0034708	cellular_component	methyltransferase complex
B	0042802	molecular_function	identical protein binding
B	0046498	biological_process	S-adenosylhomocysteine metabolic process
B	0046500	biological_process	S-adenosylmethionine metabolic process
B	0051289	biological_process	protein homotetramerization
B	0098603	molecular_function	selenol Se-methyltransferase activity
B	0170033	biological_process	L-amino acid metabolic process
B	0170039	biological_process	proteinogenic amino acid metabolic process
B	1901052	biological_process	sarcosine metabolic process
B	1904047	molecular_function	S-adenosyl-L-methionine binding
C	0005542	molecular_function	folic acid binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005977	biological_process	glycogen metabolic process
C	0006111	biological_process	regulation of gluconeogenesis
C	0006544	biological_process	glycine metabolic process
C	0006555	biological_process	methionine metabolic process
C	0006730	biological_process	one-carbon metabolic process
C	0008168	molecular_function	methyltransferase activity
C	0008757	molecular_function	S-adenosylmethionine-dependent methyltransferase activity
C	0016594	molecular_function	glycine binding
C	0016740	molecular_function	transferase activity
C	0017174	molecular_function	glycine N-methyltransferase activity
C	0032259	biological_process	methylation
C	0034708	cellular_component	methyltransferase complex
C	0042802	molecular_function	identical protein binding
C	0046498	biological_process	S-adenosylhomocysteine metabolic process
C	0046500	biological_process	S-adenosylmethionine metabolic process
C	0051289	biological_process	protein homotetramerization
C	0098603	molecular_function	selenol Se-methyltransferase activity
C	0170033	biological_process	L-amino acid metabolic process
C	0170039	biological_process	proteinogenic amino acid metabolic process
C	1901052	biological_process	sarcosine metabolic process
C	1904047	molecular_function	S-adenosyl-L-methionine binding
D	0005542	molecular_function	folic acid binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005977	biological_process	glycogen metabolic process
D	0006111	biological_process	regulation of gluconeogenesis
D	0006544	biological_process	glycine metabolic process
D	0006555	biological_process	methionine metabolic process
D	0006730	biological_process	one-carbon metabolic process
D	0008168	molecular_function	methyltransferase activity
D	0008757	molecular_function	S-adenosylmethionine-dependent methyltransferase activity
D	0016594	molecular_function	glycine binding
D	0016740	molecular_function	transferase activity
D	0017174	molecular_function	glycine N-methyltransferase activity
D	0032259	biological_process	methylation
D	0034708	cellular_component	methyltransferase complex
D	0042802	molecular_function	identical protein binding
D	0046498	biological_process	S-adenosylhomocysteine metabolic process
D	0046500	biological_process	S-adenosylmethionine metabolic process
D	0051289	biological_process	protein homotetramerization
D	0098603	molecular_function	selenol Se-methyltransferase activity
D	0170033	biological_process	L-amino acid metabolic process
D	0170039	biological_process	proteinogenic amino acid metabolic process
D	1901052	biological_process	sarcosine metabolic process
D	1904047	molecular_function	S-adenosyl-L-methionine binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE BME B 400

Chain	Residue
B	CYS185
B	ILE202
B	THR203
B	THR204
D	ASN210
D	GLY276
D	ALA278

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE TAM B 293

Chain	Residue
B	ILE34
B	GLY137
B	HIS142
B	ASN191
B	TYR242
A	GLU15
B	TYR33

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR CHAIN E OF 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE

Chain	Residue
A	TYR5
A	THR7
B	SER205
B	LEU207
B	THR217
B	ARG239
C	SER3
C	VAL4
C	TYR5
D	LEU207
D	HIS214
D	MET215

site_id	AC4
Number of Residues	12
Details	BINDING SITE FOR CHAIN F OF 5-METHYLTETRAHYDROFOLATE PENTAGLUTAMATE

Chain	Residue
A	LEU207
A	HIS214
A	MET215
B	SER3
B	VAL4
B	TYR5
C	SER146
C	HIS214
C	MET215
C	ARG239
D	TYR5
D	ARG6

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22037183","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3THR","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"3THS","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22037183","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3THS","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12859184","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1NBH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1NBI","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8810903","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1XVA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Modified residue: {"description":"N-acetylvaline","evidences":[{"source":"PubMed","id":"2822402","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	16
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q9QXF8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	5
Details	M-CSA 23

Chain	Residue	Details
A	GLU25	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
A	ALA141	electrostatic stabiliser, hydrogen bond acceptor
A	SER146	activator
A	TYR179	electrostatic stabiliser
A	LEU198	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

site_id	MCSA2
Number of Residues	5
Details	M-CSA 23

Chain	Residue	Details
B	GLU25	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
B	ALA141	electrostatic stabiliser, hydrogen bond acceptor
B	SER146	activator
B	TYR179	electrostatic stabiliser
B	LEU198	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

site_id	MCSA3
Number of Residues	5
Details	M-CSA 23

Chain	Residue	Details
C	GLU25	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
C	ALA141	electrostatic stabiliser, hydrogen bond acceptor
C	SER146	activator
C	TYR179	electrostatic stabiliser
C	LEU198	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

site_id	MCSA4
Number of Residues	5
Details	M-CSA 23

Chain	Residue	Details
D	GLU25	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
D	ALA141	electrostatic stabiliser, hydrogen bond acceptor
D	SER146	activator
D	TYR179	electrostatic stabiliser
D	LEU198	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)