6FDC
Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a
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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue ZN A 601 |
| Chain | Residue |
| A | HIS330 |
| A | HIS366 |
| A | ASP367 |
| A | ASP484 |
| A | HOH725 |
| A | HOH839 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 602 |
| Chain | Residue |
| A | HOH798 |
| A | HOH815 |
| A | HOH895 |
| A | ASP367 |
| A | HOH725 |
| A | HOH769 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 603 |
| Chain | Residue |
| A | ASP467 |
| A | ASP471 |
| A | HIS527 |
| A | HOH742 |
| A | HOH783 |
| A | HOH831 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue MG A 604 |
| Chain | Residue |
| A | ASN417 |
| A | HOH842 |
| A | HOH867 |
| A | HOH918 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 605 |
| Chain | Residue |
| A | LYS428 |
| A | ASP432 |
| A | HOH763 |
| site_id | AC6 |
| Number of Residues | 17 |
| Details | binding site for residue DD5 A 606 |
| Chain | Residue |
| A | TYR325 |
| A | SER374 |
| A | ASN487 |
| A | PRO488 |
| A | TYR495 |
| A | TRP498 |
| A | THR499 |
| A | ILE502 |
| A | PHE506 |
| A | PRO522 |
| A | MET523 |
| A | CYS524 |
| A | SER534 |
| A | GLN535 |
| A | PHE538 |
| A | HOH701 |
| A | HOH768 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 601 |
| Chain | Residue |
| B | HIS330 |
| B | HIS366 |
| B | ASP367 |
| B | ASP484 |
| B | HOH720 |
| B | HOH838 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 602 |
| Chain | Residue |
| B | ASP367 |
| B | HOH720 |
| B | HOH762 |
| B | HOH793 |
| B | HOH799 |
| B | HOH871 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 603 |
| Chain | Residue |
| A | HOH778 |
| A | HOH932 |
| A | HOH943 |
| B | HOH730 |
| B | HOH754 |
| B | HOH891 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 604 |
| Chain | Residue |
| A | ASN390 |
| A | HOH764 |
| B | LYS428 |
| B | ILE431 |
| B | ASP432 |
| site_id | AD2 |
| Number of Residues | 13 |
| Details | binding site for residue D5N B 605 |
| Chain | Residue |
| B | TYR325 |
| B | ASN487 |
| B | PRO488 |
| B | TYR495 |
| B | TRP498 |
| B | THR499 |
| B | PHE506 |
| B | MET523 |
| B | SER534 |
| B | GLN535 |
| B | PHE538 |
| B | ILE542 |
| B | HOH705 |
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 | HIS366-PHE377 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"Q07343","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)"} |
| Chain | Residue | Details |
