6AKR
Crystal structure of the PDE4D catalytic domain in complex with osthole
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| A | 0007165 | biological_process | signal transduction |
| A | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| B | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| B | 0007165 | biological_process | signal transduction |
| B | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| C | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| C | 0007165 | biological_process | signal transduction |
| C | 0008081 | molecular_function | phosphoric diester hydrolase activity |
| D | 0004114 | molecular_function | 3',5'-cyclic-nucleotide phosphodiesterase activity |
| D | 0007165 | biological_process | signal transduction |
| D | 0008081 | molecular_function | phosphoric diester hydrolase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue ZN A 701 |
| Chain | Residue |
| A | HIS402 |
| A | HIS438 |
| A | ASP439 |
| A | ASP556 |
| A | ZN702 |
| A | HOH860 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue ZN A 702 |
| Chain | Residue |
| A | HOH826 |
| A | HOH830 |
| A | HOH880 |
| A | ASP439 |
| A | ZN701 |
| A | HOH823 |
| site_id | AC3 |
| Number of Residues | 9 |
| Details | binding site for residue A0O A 703 |
| Chain | Residue |
| A | TYR397 |
| A | ASN559 |
| A | TYR567 |
| A | THR571 |
| A | MET575 |
| A | PHE578 |
| A | MET595 |
| A | GLN607 |
| A | PHE610 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 701 |
| Chain | Residue |
| B | HIS402 |
| B | HIS438 |
| B | ASP439 |
| B | ASP556 |
| B | ZN702 |
| B | HOH880 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 702 |
| Chain | Residue |
| B | ASP439 |
| B | ZN701 |
| B | HOH808 |
| B | HOH827 |
| B | HOH836 |
| B | HOH870 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue A0O B 703 |
| Chain | Residue |
| B | TYR397 |
| B | ASN559 |
| B | THR571 |
| B | ILE574 |
| B | PHE578 |
| B | MET595 |
| B | GLN607 |
| B | PHE610 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 701 |
| Chain | Residue |
| C | HIS402 |
| C | HIS438 |
| C | ASP439 |
| C | ASP556 |
| C | ZN702 |
| C | HOH860 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 702 |
| Chain | Residue |
| C | ASP439 |
| C | ZN701 |
| C | HOH801 |
| C | HOH814 |
| C | HOH836 |
| C | HOH840 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | binding site for residue A0O C 703 |
| Chain | Residue |
| C | TYR397 |
| C | ASN559 |
| C | THR571 |
| C | ILE574 |
| C | MET595 |
| C | GLN607 |
| C | PHE610 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 701 |
| Chain | Residue |
| D | HIS402 |
| D | HIS438 |
| D | ASP439 |
| D | ASP556 |
| D | ZN702 |
| D | HOH878 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 702 |
| Chain | Residue |
| D | ASP439 |
| D | ZN701 |
| D | HOH818 |
| D | HOH819 |
| D | HOH831 |
| D | HOH874 |
| site_id | AD3 |
| Number of Residues | 7 |
| Details | binding site for residue A0O D 703 |
| Chain | Residue |
| D | ASN559 |
| D | TYR567 |
| D | THR571 |
| D | PHE578 |
| D | MET595 |
| D | GLN607 |
| D | PHE610 |
Functional Information from PROSITE/UniProt
| site_id | PS00126 |
| Number of Residues | 12 |
| Details | PDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDVdHpGvsNqF |
| Chain | Residue | Details |
| A | HIS438-PHE449 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000250|UniProtKB:Q07343 |
| Chain | Residue | Details |
| A | HIS398 | |
| B | HIS398 | |
| C | HIS398 | |
| D | HIS398 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7 |
| Chain | Residue | Details |
| A | HIS398 | |
| D | HIS398 | |
| D | ASN559 | |
| D | GLN607 | |
| A | ASN559 | |
| A | GLN607 | |
| B | HIS398 | |
| B | ASN559 | |
| B | GLN607 | |
| C | HIS398 | |
| C | ASN559 | |
| C | GLN607 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:2PW3 |
| Chain | Residue | Details |
| A | HIS402 | |
| B | HIS402 | |
| C | HIS402 | |
| D | HIS402 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0000269|PubMed:15576036, ECO:0000269|PubMed:17582435, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7, ECO:0007744|PDB:1TBB, ECO:0007744|PDB:1XOM, ECO:0007744|PDB:1XON, ECO:0007744|PDB:1XOQ, ECO:0007744|PDB:1XOR, ECO:0007744|PDB:2PW3 |
| Chain | Residue | Details |
| A | HIS438 | |
| A | ASP556 | |
| B | HIS438 | |
| B | ASP556 | |
| C | HIS438 | |
| C | ASP556 | |
| D | HIS438 | |
| D | ASP556 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW |
| Chain | Residue | Details |
| A | ASP439 | |
| A | PHE610 | |
| B | ASP439 | |
| B | PHE610 | |
| C | ASP439 | |
| C | PHE610 | |
| D | ASP439 | |
| D | PHE610 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) |
| Chain | Residue | Details |
| A | LYS323 | |
| B | LYS323 | |
| C | LYS323 | |
| D | LYS323 |
