5LNU
Crystal structure of Arabidopsis thaliana Pdx1-I320 complex
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006520 | biological_process | amino acid metabolic process |
| A | 0006979 | biological_process | response to oxidative stress |
| A | 0006982 | biological_process | response to lipid hydroperoxide |
| A | 0009651 | biological_process | response to salt stress |
| A | 0010224 | biological_process | response to UV-B |
| A | 0010335 | biological_process | response to non-ionic osmotic stress |
| A | 0012505 | cellular_component | endomembrane system |
| A | 0015994 | biological_process | chlorophyll metabolic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| A | 0042538 | biological_process | hyperosmotic salinity response |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0042819 | biological_process | vitamin B6 biosynthetic process |
| A | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006520 | biological_process | amino acid metabolic process |
| B | 0006979 | biological_process | response to oxidative stress |
| B | 0006982 | biological_process | response to lipid hydroperoxide |
| B | 0009651 | biological_process | response to salt stress |
| B | 0010224 | biological_process | response to UV-B |
| B | 0010335 | biological_process | response to non-ionic osmotic stress |
| B | 0012505 | cellular_component | endomembrane system |
| B | 0015994 | biological_process | chlorophyll metabolic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| B | 0042538 | biological_process | hyperosmotic salinity response |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0042819 | biological_process | vitamin B6 biosynthetic process |
| B | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0005886 | cellular_component | plasma membrane |
| C | 0006520 | biological_process | amino acid metabolic process |
| C | 0006979 | biological_process | response to oxidative stress |
| C | 0006982 | biological_process | response to lipid hydroperoxide |
| C | 0009651 | biological_process | response to salt stress |
| C | 0010224 | biological_process | response to UV-B |
| C | 0010335 | biological_process | response to non-ionic osmotic stress |
| C | 0012505 | cellular_component | endomembrane system |
| C | 0015994 | biological_process | chlorophyll metabolic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| C | 0042538 | biological_process | hyperosmotic salinity response |
| C | 0042803 | molecular_function | protein homodimerization activity |
| C | 0042819 | biological_process | vitamin B6 biosynthetic process |
| C | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0005886 | cellular_component | plasma membrane |
| D | 0006520 | biological_process | amino acid metabolic process |
| D | 0006979 | biological_process | response to oxidative stress |
| D | 0006982 | biological_process | response to lipid hydroperoxide |
| D | 0009651 | biological_process | response to salt stress |
| D | 0010224 | biological_process | response to UV-B |
| D | 0010335 | biological_process | response to non-ionic osmotic stress |
| D | 0012505 | cellular_component | endomembrane system |
| D | 0015994 | biological_process | chlorophyll metabolic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0036381 | molecular_function | pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity |
| D | 0042538 | biological_process | hyperosmotic salinity response |
| D | 0042803 | molecular_function | protein homodimerization activity |
| D | 0042819 | biological_process | vitamin B6 biosynthetic process |
| D | 0042823 | biological_process | pyridoxal phosphate biosynthetic process |
| D | 0046982 | molecular_function | protein heterodimerization activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 13 |
| Details | binding site for residue PO4 A 401 |
| Chain | Residue |
| A | PRO66 |
| A | HOH505 |
| A | HOH508 |
| A | HOH543 |
| A | HOH619 |
| A | LYS166 |
| A | GLU168 |
| A | GLY170 |
| A | GLY230 |
| A | GLY231 |
| A | GLY252 |
| A | SER253 |
| A | KIK403 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | binding site for residue SO4 A 402 |
| Chain | Residue |
| A | HIS132 |
| A | GLU151 |
| A | ARG154 |
| A | ARG155 |
| A | HOH533 |
| A | HOH544 |
| A | HOH583 |
| A | HOH586 |
| A | HOH613 |
| D | LYS204 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue KIK A 403 |
| Chain | Residue |
| A | ASP41 |
| A | LYS98 |
| A | SER121 |
| A | VAL123 |
| A | ARG164 |
| A | LYS166 |
| A | PO4401 |
| site_id | AC4 |
| Number of Residues | 13 |
| Details | binding site for residue PO4 B 401 |
| Chain | Residue |
| B | PRO66 |
| B | LYS166 |
| B | GLU168 |
| B | GLY170 |
| B | GLY230 |
| B | GLY231 |
| B | GLY252 |
| B | SER253 |
| B | KIK403 |
| B | HOH506 |
| B | HOH508 |
| B | HOH545 |
| B | HOH623 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 B 402 |
| Chain | Residue |
| B | HIS132 |
| B | GLU151 |
| B | ARG154 |
| B | ARG155 |
| B | HOH551 |
| B | HOH636 |
| C | LYS204 |
| C | HOH634 |
| site_id | AC6 |
| Number of Residues | 14 |
| Details | binding site for residue PO4 C 401 |
| Chain | Residue |
| C | PRO66 |
| C | LYS166 |
| C | GLU168 |
| C | ALA169 |
| C | GLY170 |
| C | GLY230 |
| C | GLY231 |
| C | GLY252 |
| C | SER253 |
| C | KIK403 |
| C | HOH501 |
| C | HOH502 |
| C | HOH558 |
| C | HOH635 |
| site_id | AC7 |
| Number of Residues | 11 |
| Details | binding site for residue SO4 C 402 |
| Chain | Residue |
| B | LYS204 |
| C | HIS132 |
| C | GLU151 |
| C | ARG154 |
| C | ARG155 |
| C | HOH507 |
| C | HOH528 |
| C | HOH602 |
| C | HOH604 |
| C | HOH613 |
| C | HOH668 |
| site_id | AC8 |
| Number of Residues | 14 |
| Details | binding site for residue PO4 D 401 |
| Chain | Residue |
| D | PRO66 |
| D | LYS166 |
| D | GLU168 |
| D | ALA169 |
| D | GLY170 |
| D | GLY230 |
| D | GLY231 |
| D | GLY252 |
| D | SER253 |
| D | KIK403 |
| D | HOH509 |
| D | HOH514 |
| D | HOH584 |
| D | HOH599 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 D 402 |
| Chain | Residue |
| A | LYS204 |
| D | HIS132 |
| D | GLU151 |
| D | ARG154 |
| D | ARG155 |
| D | HOH547 |
| D | HOH565 |
| D | HOH593 |
| D | HOH628 |
| site_id | AD1 |
| Number of Residues | 15 |
| Details | binding site for Di-peptide KIK B 403 and LYS B 98 |
| Chain | Residue |
| B | ASP41 |
| B | MET60 |
| B | ALA61 |
| B | MET78 |
| B | ALA97 |
| B | ALA99 |
| B | LEU110 |
| B | ASP119 |
| B | SER121 |
| B | VAL123 |
| B | LEU124 |
| B | ARG164 |
| B | LYS166 |
| B | PO4401 |
| B | HOH531 |
| site_id | AD2 |
| Number of Residues | 13 |
| Details | binding site for Di-peptide KIK B 403 and LYS B 166 |
| Chain | Residue |
| B | ASP41 |
| B | LYS98 |
| B | SER121 |
| B | GLU122 |
| B | VAL123 |
| B | CYS146 |
| B | ARG164 |
| B | THR165 |
| B | GLY167 |
| B | ALA169 |
| B | HIS180 |
| B | ALA229 |
| B | PO4401 |
| site_id | AD3 |
| Number of Residues | 13 |
| Details | binding site for Di-peptide KIK C 403 and LYS C 166 |
| Chain | Residue |
| C | ASP41 |
| C | LYS98 |
| C | SER121 |
| C | GLU122 |
| C | VAL123 |
| C | CYS146 |
| C | ARG164 |
| C | THR165 |
| C | GLY167 |
| C | HIS180 |
| C | ALA229 |
| C | GLY230 |
| C | PO4401 |
| site_id | AD4 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide KIK C 403 and LYS C 98 |
| Chain | Residue |
| C | ASP41 |
| C | MET60 |
| C | ALA61 |
| C | ALA97 |
| C | ALA99 |
| C | LEU110 |
| C | ASP119 |
| C | SER121 |
| C | VAL123 |
| C | LEU124 |
| C | ARG164 |
| C | LYS166 |
| C | PO4401 |
| C | HOH569 |
| site_id | AD5 |
| Number of Residues | 13 |
| Details | binding site for Di-peptide KIK D 403 and LYS D 166 |
| Chain | Residue |
| D | ASP41 |
| D | LYS98 |
| D | SER121 |
| D | GLU122 |
| D | VAL123 |
| D | CYS146 |
| D | ARG164 |
| D | THR165 |
| D | GLY167 |
| D | ALA169 |
| D | HIS180 |
| D | ALA229 |
| D | PO4401 |
| site_id | AD6 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide KIK D 403 and LYS D 98 |
| Chain | Residue |
| D | ASP41 |
| D | MET60 |
| D | ALA61 |
| D | ALA97 |
| D | ALA99 |
| D | LEU110 |
| D | ASP119 |
| D | SER121 |
| D | VAL123 |
| D | LEU124 |
| D | ARG164 |
| D | LYS166 |
| D | PO4401 |
| D | HOH578 |
Functional Information from PROSITE/UniProt
| site_id | PS01235 |
| Number of Residues | 19 |
| Details | PDXS_SNZ_1 PdxS/SNZ family signature. LPVVQFAAGGVATPADAAL |
| Chain | Residue | Details |
| A | LEU222-LEU240 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Schiff-base intermediate with D-ribose 5-phosphate => ECO:0000250|UniProtKB:O59080 |
| Chain | Residue | Details |
| A | LYS98 | |
| B | LYS98 | |
| C | LYS98 | |
| D | LYS98 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:O59080 |
| Chain | Residue | Details |
| A | ASP41 | |
| C | GLY170 | |
| C | GLY231 | |
| C | GLY252 | |
| D | ASP41 | |
| D | GLY170 | |
| D | GLY231 | |
| D | GLY252 | |
| A | GLY170 | |
| A | GLY231 | |
| A | GLY252 | |
| B | ASP41 | |
| B | GLY170 | |
| B | GLY231 | |
| B | GLY252 | |
| C | ASP41 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q03148 |
| Chain | Residue | Details |
| A | ARG182 | |
| B | ARG182 | |
| C | ARG182 | |
| D | ARG182 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:22223895 |
| Chain | Residue | Details |
| A | MET2 | |
| B | MET2 | |
| C | MET2 | |
| D | MET2 |
