2IDK
Crystal Structure of Rat Glycine N-Methyltransferase Complexed With Folate
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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 12 |
Details | BINDING SITE FOR RESIDUE C2F A 1410 |
Chain | Residue |
A | TYR5 |
D | LEU207 |
D | HIS214 |
D | MET215 |
A | THR7 |
B | LEU207 |
B | HIS214 |
B | MET215 |
B | ARG239 |
C | SER3 |
C | VAL4 |
C | TYR5 |
site_id | AC2 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE C2F B 1420 |
Chain | Residue |
A | LEU207 |
A | MET215 |
B | SER3 |
B | TYR5 |
C | LEU207 |
C | HIS214 |
C | MET215 |
C | ARG239 |
D | TYR5 |
D | THR7 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:22037183, ECO:0000312|PDB:3THR, ECO:0000312|PDB:3THS |
Chain | Residue | Details |
A | VAL4 | |
D | VAL4 | |
D | MET215 | |
D | LEU240 | |
A | MET215 | |
A | LEU240 | |
B | VAL4 | |
B | MET215 | |
B | LEU240 | |
C | VAL4 | |
C | MET215 | |
C | LEU240 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:22037183, ECO:0000312|PDB:3THS |
Chain | Residue | Details |
A | ARG6 | |
B | ARG6 | |
C | ARG6 | |
D | ARG6 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0007744|PDB:1NBH |
Chain | Residue | Details |
A | ALA22 | |
B | ALA22 | |
C | ALA22 | |
D | ALA22 |
site_id | SWS_FT_FI4 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0007744|PDB:1NBH, ECO:0007744|PDB:1NBI |
Chain | Residue | Details |
A | GLN31 | |
C | THR41 | |
C | ALA86 | |
C | TRP117 | |
D | GLN31 | |
D | THR41 | |
D | ALA86 | |
D | TRP117 | |
A | THR41 | |
A | ALA86 | |
A | TRP117 | |
B | GLN31 | |
B | THR41 | |
B | ALA86 | |
B | TRP117 | |
C | GLN31 |
site_id | SWS_FT_FI5 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8810903, ECO:0007744|PDB:1XVA |
Chain | Residue | Details |
A | ILE34 | |
D | ILE34 | |
D | ASN176 | |
D | THR221 | |
A | ASN176 | |
A | THR221 | |
B | ILE34 | |
B | ASN176 | |
B | THR221 | |
C | ILE34 | |
C | ASN176 | |
C | THR221 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0000269|PubMed:8810903, ECO:0000312|PDB:1XVA, ECO:0007744|PDB:1NBH, ECO:0007744|PDB:1NBI |
Chain | Residue | Details |
A | CYS65 | |
B | CYS65 | |
C | CYS65 | |
D | CYS65 |
site_id | SWS_FT_FI7 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:12859184, ECO:0000269|PubMed:8810903, ECO:0007744|PDB:1NBI, ECO:0007744|PDB:1XVA |
Chain | Residue | Details |
A | GLY137 | |
B | GLY137 | |
C | GLY137 | |
D | GLY137 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | MOD_RES: N-acetylvaline => ECO:0000269|PubMed:2822402 |
Chain | Residue | Details |
A | ASP2 | |
B | ASP2 | |
C | ASP2 | |
D | ASP2 |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q9QXF8 |
Chain | Residue | Details |
A | LEU10 | |
B | LEU10 | |
C | LEU10 | |
D | LEU10 |
site_id | SWS_FT_FI10 |
Number of Residues | 4 |
Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q9QXF8 |
Chain | Residue | Details |
A | ILE34 | |
B | ILE34 | |
C | ILE34 | |
D | ILE34 |
site_id | SWS_FT_FI11 |
Number of Residues | 16 |
Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:Q9QXF8 |
Chain | Residue | Details |
A | ALA46 | |
C | ASN191 | |
C | SER196 | |
C | ASP201 | |
D | ALA46 | |
D | ASN191 | |
D | SER196 | |
D | ASP201 | |
A | ASN191 | |
A | SER196 | |
A | ASP201 | |
B | ALA46 | |
B | ASN191 | |
B | SER196 | |
B | ASP201 | |
C | ALA46 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1xva |
Chain | Residue | Details |
A | GLU15 |
site_id | CSA2 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1xva |
Chain | Residue | Details |
B | GLU15 |
site_id | CSA3 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1xva |
Chain | Residue | Details |
C | GLU15 |
site_id | CSA4 |
Number of Residues | 1 |
Details | Annotated By Reference To The Literature 1xva |
Chain | Residue | Details |
D | GLU15 |
site_id | MCSA1 |
Number of Residues | 5 |
Details | M-CSA 23 |
Chain | Residue | Details |
A | ALA22 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
A | ASN138 | electrostatic stabiliser, hydrogen bond acceptor |
A | LEU143 | activator |
A | ASN176 | electrostatic stabiliser |
A | LYS195 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
site_id | MCSA2 |
Number of Residues | 5 |
Details | M-CSA 23 |
Chain | Residue | Details |
B | ALA22 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
B | ASN138 | electrostatic stabiliser, hydrogen bond acceptor |
B | LEU143 | activator |
B | ASN176 | electrostatic stabiliser |
B | LYS195 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
site_id | MCSA3 |
Number of Residues | 5 |
Details | M-CSA 23 |
Chain | Residue | Details |
C | ALA22 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
C | ASN138 | electrostatic stabiliser, hydrogen bond acceptor |
C | LEU143 | activator |
C | ASN176 | electrostatic stabiliser |
C | LYS195 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
site_id | MCSA4 |
Number of Residues | 5 |
Details | M-CSA 23 |
Chain | Residue | Details |
D | ALA22 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
D | ASN138 | electrostatic stabiliser, hydrogen bond acceptor |
D | LEU143 | activator |
D | ASN176 | electrostatic stabiliser |
D | LYS195 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |