4FIR
Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0016829 | molecular_function | lyase activity |
| A | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| A | 0042819 | biological_process | vitamin B6 biosynthetic process |
| A | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| B | 0042819 | biological_process | vitamin B6 biosynthetic process |
| B | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| C | 0042819 | biological_process | vitamin B6 biosynthetic process |
| C | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| D | 0042819 | biological_process | vitamin B6 biosynthetic process |
| D | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| E | 0016829 | molecular_function | lyase activity |
| E | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| E | 0042819 | biological_process | vitamin B6 biosynthetic process |
| E | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| F | 0016829 | molecular_function | lyase activity |
| F | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| F | 0042819 | biological_process | vitamin B6 biosynthetic process |
| F | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE R5P A 401 |
| Chain | Residue |
| A | ASP30 |
| A | GLY278 |
| A | SER279 |
| A | PRO55 |
| A | LYS87 |
| A | SER110 |
| A | ARG153 |
| A | ALA158 |
| A | GLY159 |
| A | GLY256 |
| A | GLY257 |
| site_id | AC2 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE R5P B 401 |
| Chain | Residue |
| B | ASP30 |
| B | PRO55 |
| B | LYS87 |
| B | ASP108 |
| B | SER110 |
| B | VAL112 |
| B | ARG153 |
| B | ALA158 |
| B | GLY159 |
| B | GLY256 |
| B | GLY257 |
| B | VAL277 |
| B | GLY278 |
| B | SER279 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE R5P C 401 |
| Chain | Residue |
| C | ASP30 |
| C | LYS87 |
| C | ASP108 |
| C | ARG153 |
| C | ALA158 |
| C | GLY159 |
| C | GLY256 |
| C | GLY257 |
| C | GLY278 |
| C | SER279 |
| site_id | AC4 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE R5P D 401 |
| Chain | Residue |
| D | ASP30 |
| D | PRO55 |
| D | LYS87 |
| D | ASP108 |
| D | SER110 |
| D | VAL112 |
| D | ALA158 |
| D | GLY159 |
| D | GLY256 |
| D | GLY257 |
| D | VAL277 |
| D | GLY278 |
| D | SER279 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE R5P E 401 |
| Chain | Residue |
| E | ASP30 |
| E | PRO55 |
| E | LYS87 |
| E | ASP108 |
| E | VAL112 |
| E | ARG153 |
| E | ALA158 |
| E | GLY159 |
| E | GLY256 |
| E | GLY257 |
| E | VAL277 |
| E | GLY278 |
| E | SER279 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE R5P F 401 |
| Chain | Residue |
| F | ASP30 |
| F | LYS87 |
| F | ARG153 |
| F | ALA158 |
| F | GLY159 |
| F | GLY256 |
| F | GLY257 |
| F | GLY278 |
| F | SER279 |
Functional Information from PROSITE/UniProt
| site_id | PS01235 |
| Number of Residues | 19 |
| Details | PDXS_SNZ_1 PdxS/SNZ family signature. LPVVNFAAGGVATPADAAL |
| Chain | Residue | Details |
| A | LEU248-LEU266 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | ACT_SITE: Schiff-base intermediate with D-ribose 5-phosphate => ECO:0000255|HAMAP-Rule:MF_01824, ECO:0000269|PubMed:23104439 |
| Chain | Residue | Details |
| A | LYS87 | |
| B | LYS87 | |
| C | LYS87 | |
| D | LYS87 | |
| E | LYS87 | |
| F | LYS87 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01824, ECO:0000269|PubMed:23104439 |
| Chain | Residue | Details |
| A | ASP30 | |
| C | GLY159 | |
| C | GLY257 | |
| C | GLY278 | |
| D | ASP30 | |
| D | GLY159 | |
| D | GLY257 | |
| D | GLY278 | |
| E | ASP30 | |
| E | GLY159 | |
| E | GLY257 | |
| A | GLY159 | |
| E | GLY278 | |
| F | ASP30 | |
| F | GLY159 | |
| F | GLY257 | |
| F | GLY278 | |
| A | GLY257 | |
| A | GLY278 | |
| B | ASP30 | |
| B | GLY159 | |
| B | GLY257 | |
| B | GLY278 | |
| C | ASP30 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01824 |
| Chain | Residue | Details |
| A | ARG171 | |
| B | ARG171 | |
| C | ARG171 | |
| D | ARG171 | |
| E | ARG171 | |
| F | ARG171 |
