6NJJ
Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770
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 | HIS330 |
| A | HIS366 |
| A | ASP367 |
| A | ASP484 |
| A | HOH805 |
| A | HOH823 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 702 |
| Chain | Residue |
| A | HOH869 |
| A | HOH894 |
| A | HOH907 |
| A | ASP367 |
| A | HOH807 |
| A | HOH823 |
| site_id | AC3 |
| Number of Residues | 14 |
| Details | binding site for residue KR7 A 703 |
| Chain | Residue |
| A | TYR325 |
| A | MET439 |
| A | ASN487 |
| A | TYR495 |
| A | TRP498 |
| A | THR499 |
| A | ILE502 |
| A | GLN535 |
| A | PHE538 |
| A | PHE599 |
| A | THR603 |
| A | HOH836 |
| A | HOH875 |
| A | HOH880 |
| site_id | AC4 |
| Number of Residues | 11 |
| Details | binding site for residue BTB A 704 |
| Chain | Residue |
| A | HIS318 |
| A | GLU409 |
| A | ZN705 |
| A | HOH817 |
| A | HOH828 |
| A | HOH892 |
| C | HIS320 |
| C | ASP322 |
| C | ASP369 |
| C | PRO371 |
| C | ARG512 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue ZN A 705 |
| Chain | Residue |
| A | HIS318 |
| A | BTB704 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 706 |
| Chain | Residue |
| A | HIS271 |
| A | VAL272 |
| A | PHE273 |
| A | ARG274 |
| A | LEU494 |
| A | GLN497 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 707 |
| Chain | Residue |
| A | LEU341 |
| A | THR344 |
| A | TRP550 |
| A | ASP557 |
| A | ILE561 |
| A | HOH866 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 701 |
| Chain | Residue |
| B | HIS330 |
| B | HIS366 |
| B | ASP367 |
| B | ASP484 |
| B | HOH829 |
| B | HOH830 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 702 |
| Chain | Residue |
| B | ASP367 |
| B | HOH817 |
| B | HOH829 |
| B | HOH847 |
| B | HOH874 |
| B | HOH883 |
| site_id | AD1 |
| Number of Residues | 13 |
| Details | binding site for residue KR7 B 703 |
| Chain | Residue |
| B | TYR325 |
| B | MET439 |
| B | ASN487 |
| B | TYR495 |
| B | TRP498 |
| B | THR499 |
| B | ILE502 |
| B | GLN535 |
| B | PHE538 |
| B | PHE599 |
| B | HOH805 |
| B | HOH862 |
| B | HOH870 |
| site_id | AD2 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 B 704 |
| Chain | Residue |
| B | HIS271 |
| B | VAL272 |
| B | PHE273 |
| B | ARG274 |
| B | GLN493 |
| B | LEU494 |
| B | GLN497 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 701 |
| Chain | Residue |
| C | HIS330 |
| C | HIS366 |
| C | ASP367 |
| C | ASP484 |
| C | HOH833 |
| C | HOH867 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 702 |
| Chain | Residue |
| C | ASP367 |
| C | HOH828 |
| C | HOH833 |
| C | HOH849 |
| C | HOH903 |
| C | HOH912 |
| site_id | AD5 |
| Number of Residues | 13 |
| Details | binding site for residue KR7 C 703 |
| Chain | Residue |
| C | TRP498 |
| C | THR499 |
| C | ILE502 |
| C | GLN535 |
| C | PHE538 |
| C | PHE599 |
| C | HOH843 |
| C | HOH860 |
| C | HOH902 |
| C | TYR325 |
| C | MET439 |
| C | ASN487 |
| C | TYR495 |
| site_id | AD6 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 C 704 |
| Chain | Residue |
| C | HIS271 |
| C | VAL272 |
| C | PHE273 |
| C | ARG274 |
| C | GLN493 |
| C | LEU494 |
| C | GLN497 |
| C | HOH839 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 701 |
| Chain | Residue |
| D | HIS330 |
| D | HIS366 |
| D | ASP367 |
| D | ASP484 |
| D | HOH817 |
| D | HOH870 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 702 |
| Chain | Residue |
| D | ASP367 |
| D | HOH804 |
| D | HOH817 |
| D | HOH856 |
| D | HOH857 |
| D | HOH895 |
| site_id | AD9 |
| Number of Residues | 13 |
| Details | binding site for residue KR7 D 703 |
| Chain | Residue |
| D | TYR325 |
| D | MET439 |
| D | ASN487 |
| D | TYR495 |
| D | TRP498 |
| D | THR499 |
| D | ILE502 |
| D | GLN535 |
| D | PHE538 |
| D | PHE599 |
| D | HOH833 |
| D | HOH855 |
| D | HOH862 |
| site_id | AE1 |
| Number of Residues | 7 |
| Details | binding site for residue BTB D 704 |
| Chain | Residue |
| B | HIS320 |
| B | ASP322 |
| B | HOH809 |
| D | HIS318 |
| D | GLU409 |
| D | ZN705 |
| D | HOH803 |
| site_id | AE2 |
| Number of Residues | 2 |
| Details | binding site for residue ZN D 705 |
| Chain | Residue |
| D | HIS318 |
| D | BTB704 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 D 706 |
| Chain | Residue |
| D | HIS271 |
| D | VAL272 |
| D | PHE273 |
| D | ARG274 |
| D | LEU494 |
| D | GLN497 |
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 | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000250|UniProtKB:Q07343 |
| Chain | Residue | Details |
| A | LEU387 | |
| B | LEU387 | |
| C | LEU387 | |
| D | LEU387 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1PTW, ECO:0007744|PDB:1TB7 |
| Chain | Residue | Details |
| C | LEU387 | |
| C | GLU548 | |
| D | LEU387 | |
| D | GLU548 | |
| A | LEU387 | |
| A | GLU548 | |
| B | LEU387 | |
| B | GLU548 |
| 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 | ASP391 | |
| B | ASP391 | |
| C | ASP391 | |
| D | ASP391 |
| 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 |
| C | ARG427 | |
| C | PRO545 | |
| D | ARG427 | |
| D | PRO545 | |
| A | ARG427 | |
| A | PRO545 | |
| B | ARG427 | |
| B | PRO545 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW |
| Chain | Residue | Details |
| A | LYS428 | |
| B | LYS428 | |
| C | LYS428 | |
| D | LYS428 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| C | PHE273 | |
| C | THR300 | |
| D | PHE273 | |
| D | THR300 | |
| A | PHE273 | |
| A | THR300 | |
| B | PHE273 | |
| B | THR300 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) |
| Chain | Residue | Details |
| B | LEU312 | |
| C | LEU312 | |
| D | LEU312 | |
| A | LEU312 |
