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 |