6YMD
Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate
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 | 0006544 | biological_process | glycine metabolic process |
| A | 0006545 | biological_process | glycine biosynthetic process |
| A | 0006563 | biological_process | L-serine metabolic process |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0008168 | molecular_function | methyltransferase activity |
| 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 | 0032259 | biological_process | methylation |
| 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 | 0006544 | biological_process | glycine metabolic process |
| B | 0006545 | biological_process | glycine biosynthetic process |
| B | 0006563 | biological_process | L-serine metabolic process |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0008168 | molecular_function | methyltransferase activity |
| 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 | 0032259 | biological_process | methylation |
| B | 0035999 | biological_process | tetrahydrofolate interconversion |
| B | 0046653 | biological_process | tetrahydrofolate metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 502 |
| Chain | Residue |
| A | PRO42 |
| A | TYR416 |
| A | HOH818 |
| A | HOH873 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 503 |
| Chain | Residue |
| A | PRO133 |
| A | HIS145 |
| A | GLN332 |
| A | HOH982 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 505 |
| Chain | Residue |
| A | LEU323 |
| A | VAL326 |
| A | LEU328 |
| A | HOH800 |
| A | HOH831 |
| A | GLU142 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 503 |
| Chain | Residue |
| B | GLN21 |
| B | GLN25 |
| B | HOH635 |
| B | HOH728 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 504 |
| Chain | Residue |
| B | LYS170 |
| B | GLY196 |
| B | HOH676 |
| B | HOH740 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 505 |
| Chain | Residue |
| B | LEU86 |
| B | VAL210 |
| B | ALA211 |
| B | GLN404 |
| B | HOH601 |
| B | HOH602 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 506 |
| Chain | Residue |
| B | GLY138 |
| B | PHE141 |
| B | HOH830 |
| B | HOH857 |
| B | HOH878 |
| B | HOH969 |
| site_id | AC8 |
| Number of Residues | 22 |
| Details | binding site for residues PMP A 501 and MLI B 501 |
| Chain | Residue |
| A | SER36 |
| A | SER98 |
| A | GLY99 |
| A | ALA100 |
| A | HIS127 |
| A | SER177 |
| A | ASP202 |
| A | ALA204 |
| A | HIS205 |
| A | THR228 |
| A | HIS230 |
| A | LYS231 |
| A | ARG363 |
| A | HOH655 |
| A | HOH664 |
| A | HOH811 |
| B | TYR56 |
| B | GLU58 |
| B | TYR66 |
| B | GLY262 |
| B | GLY263 |
| B | HOH646 |
| site_id | AC9 |
| Number of Residues | 30 |
| Details | binding site for residues MLI A 504 and PMP B 502 |
| Chain | Residue |
| A | PRO42 |
| A | TYR56 |
| A | GLU58 |
| A | TYR66 |
| A | GLY262 |
| A | GLY263 |
| A | TYR416 |
| A | HOH614 |
| A | HOH818 |
| A | HOH873 |
| B | SER36 |
| B | SER98 |
| B | GLY99 |
| B | ALA100 |
| B | HIS127 |
| B | LYS170 |
| B | SER177 |
| B | GLY196 |
| B | ASP202 |
| B | ALA204 |
| B | HIS205 |
| B | THR228 |
| B | HIS230 |
| B | LYS231 |
| B | ARG363 |
| B | HOH655 |
| B | HOH676 |
| B | HOH737 |
| B | HOH740 |
| B | HOH820 |
| site_id | AD1 |
| Number of Residues | 24 |
| Details | binding site for Di-peptide PMP B 502 and LYS B 231 |
| Chain | Residue |
| B | HIS205 |
| B | THR228 |
| B | HIS230 |
| B | THR232 |
| B | LEU233 |
| B | ARG234 |
| B | HOH655 |
| B | HOH699 |
| B | HOH737 |
| B | HOH820 |
| B | HOH835 |
| A | TYR56 |
| A | GLY262 |
| A | GLY263 |
| A | MLI504 |
| B | SER36 |
| B | ASN38 |
| B | SER98 |
| B | GLY99 |
| B | ALA100 |
| B | HIS127 |
| B | SER177 |
| B | ASP202 |
| B | ALA204 |
Functional Information from PROSITE/UniProt
| site_id | PS00096 |
| Number of Residues | 17 |
| Details | SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. DVvTTTTHKTLrGPRGG |
| Chain | Residue | Details |
| A | ASP223-GLY239 |
