2DKJ
Crystal Structure of T.th.HB8 Serine Hydroxymethyltransferase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006545 | biological_process | glycine biosynthetic process |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0019264 | biological_process | glycine biosynthetic process from serine |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0035999 | biological_process | tetrahydrofolate interconversion |
| A | 0046653 | biological_process | tetrahydrofolate metabolic process |
| B | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006545 | biological_process | glycine biosynthetic process |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0008652 | biological_process | amino acid biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0019264 | biological_process | glycine biosynthetic process from serine |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0035999 | biological_process | tetrahydrofolate interconversion |
| B | 0046653 | biological_process | tetrahydrofolate metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 A 2520 |
| Chain | Residue |
| A | SER31 |
| A | SER172 |
| A | HIS200 |
| A | LYS226 |
| A | ARG358 |
| A | PLP510 |
| B | TYR61 |
| B | HOH1846 |
| site_id | AC2 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1520 |
| Chain | Residue |
| A | TYR61 |
| A | HOH2589 |
| A | HOH2597 |
| B | SER31 |
| B | SER172 |
| B | HIS200 |
| B | LYS226 |
| B | ARG358 |
| B | PLP510 |
| B | HOH1708 |
| A | TYR51 |
| site_id | AC3 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE PLP A 510 |
| Chain | Residue |
| A | SER93 |
| A | GLY94 |
| A | SER95 |
| A | HIS122 |
| A | SER172 |
| A | ASP197 |
| A | ALA199 |
| A | HIS200 |
| A | THR223 |
| A | HIS225 |
| A | LYS226 |
| A | SO42520 |
| A | HOH2530 |
| A | HOH2610 |
| B | TYR51 |
| B | GLY257 |
| B | GLY258 |
| site_id | AC4 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE PLP B 510 |
| Chain | Residue |
| A | TYR51 |
| A | GLY257 |
| A | GLY258 |
| B | SER93 |
| B | GLY94 |
| B | SER95 |
| B | HIS122 |
| B | THR124 |
| B | HIS125 |
| B | ASP197 |
| B | ALA199 |
| B | HIS200 |
| B | THR223 |
| B | HIS225 |
| B | LYS226 |
| B | SO41520 |
| B | HOH1526 |
| B | HOH1536 |
Functional Information from PROSITE/UniProt
| site_id | PS00096 |
| Number of Residues | 17 |
| Details | SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. HVvTSTTHKTLrGPRGG |
| Chain | Residue | Details |
| A | HIS218-GLY234 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of t.th.hb8 serine hydroxymethyltransferase.","authoringGroup":["RIKEN structural genomics initiative (RSGI)"]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00051","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Site: {"description":"Plays an important role in substrate specificity","evidences":[{"source":"HAMAP-Rule","id":"MF_00051","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"HAMAP-Rule","id":"MF_00051","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUL-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of t.th.hb8 serine hydroxymethyltransferase.","authoringGroup":["RIKEN structural genomics initiative (RSGI)"]}}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | ASP197 | |
| A | HIS125 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | CYS64 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | ASP197 | |
| B | HIS125 |
| site_id | CSA4 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | CYS64 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | LYS226 | |
| A | THR223 | |
| A | GLU53 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | LYS226 | |
| B | THR223 | |
| B | GLU53 |
| site_id | CSA7 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| A | LYS226 | |
| A | HIS200 |
| site_id | CSA8 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dfo |
| Chain | Residue | Details |
| B | LYS226 | |
| B | HIS200 |
