5TKB
CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH A TETRAFLUORANLINE COMPOUND
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 801 |
| Chain | Residue |
| A | HIS330 |
| A | HIS366 |
| A | ASP367 |
| A | ASP484 |
| A | HOH901 |
| A | HOH974 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 802 |
| Chain | Residue |
| A | HOH955 |
| A | HOH963 |
| A | HOH987 |
| A | ASP367 |
| A | HOH901 |
| A | HOH902 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 803 |
| Chain | Residue |
| A | HIS271 |
| A | VAL272 |
| A | PHE273 |
| A | ARG274 |
| A | LEU494 |
| A | GLN497 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue EOH A 804 |
| Chain | Residue |
| A | LYS428 |
| A | ASP432 |
| B | HOH818 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EOH A 805 |
| Chain | Residue |
| A | THR314 |
| A | HIS318 |
| A | GLU409 |
| C | PHE377 |
| C | THR381 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue EOH A 806 |
| Chain | Residue |
| A | PHE404 |
| A | ARG423 |
| A | HOH972 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | binding site for residue 7DJ A 807 |
| Chain | Residue |
| A | HIS326 |
| A | THR437 |
| A | MET439 |
| A | ASP484 |
| A | LEU485 |
| A | ASN487 |
| A | ILE502 |
| A | MET523 |
| A | GLN535 |
| A | PHE538 |
| A | HOH919 |
| A | HOH1024 |
| 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 | HOH812 |
| B | HOH854 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 702 |
| Chain | Residue |
| B | ASP367 |
| B | HOH812 |
| B | HOH814 |
| B | HOH816 |
| B | HOH826 |
| B | HOH856 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 B 703 |
| Chain | Residue |
| B | HIS271 |
| B | VAL272 |
| B | PHE273 |
| B | ARG274 |
| B | GLN493 |
| B | LEU494 |
| B | GLN497 |
| site_id | AD2 |
| Number of Residues | 1 |
| Details | binding site for residue EOH B 704 |
| Chain | Residue |
| B | PRO522 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EOH B 705 |
| Chain | Residue |
| B | HIS318 |
| B | GLU409 |
| B | HOH830 |
| D | THR381 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue EOH B 706 |
| Chain | Residue |
| A | HOH915 |
| B | LYS428 |
| B | ASP432 |
| site_id | AD5 |
| Number of Residues | 10 |
| Details | binding site for residue 7DJ B 707 |
| Chain | Residue |
| B | THR437 |
| B | MET439 |
| B | ASP484 |
| B | LEU485 |
| B | ASN487 |
| B | ILE502 |
| B | MET523 |
| B | GLN535 |
| B | PHE538 |
| B | HOH806 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 701 |
| Chain | Residue |
| C | HIS330 |
| C | HIS366 |
| C | ASP367 |
| C | ASP484 |
| C | HOH814 |
| C | HOH868 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 702 |
| Chain | Residue |
| C | ASP367 |
| C | HOH814 |
| C | HOH820 |
| C | HOH826 |
| C | HOH842 |
| C | HOH871 |
| site_id | AD8 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 C 703 |
| Chain | Residue |
| C | HIS271 |
| C | VAL272 |
| C | PHE273 |
| C | ARG274 |
| C | GLN493 |
| C | LEU494 |
| C | GLN497 |
| site_id | AD9 |
| Number of Residues | 3 |
| Details | binding site for residue EOH C 704 |
| Chain | Residue |
| D | HOH831 |
| C | LYS428 |
| C | ASP432 |
| site_id | AE1 |
| Number of Residues | 11 |
| Details | binding site for residue 7DJ C 705 |
| Chain | Residue |
| C | THR437 |
| C | MET439 |
| C | ASP484 |
| C | LEU485 |
| C | ASN487 |
| C | ILE502 |
| C | PHE506 |
| C | MET523 |
| C | GLN535 |
| C | PHE538 |
| C | HOH801 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 701 |
| Chain | Residue |
| D | HIS330 |
| D | HIS366 |
| D | ASP367 |
| D | ASP484 |
| D | HOH801 |
| D | HOH867 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 702 |
| Chain | Residue |
| D | ASP367 |
| D | HOH801 |
| D | HOH806 |
| D | HOH835 |
| D | HOH849 |
| D | HOH891 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue EOH D 703 |
| Chain | Residue |
| C | HOH822 |
| D | LYS428 |
| D | ASP432 |
| site_id | AE5 |
| Number of Residues | 12 |
| Details | binding site for residue 7DJ D 704 |
| Chain | Residue |
| D | THR437 |
| D | MET439 |
| D | ASP484 |
| D | LEU485 |
| D | ASN487 |
| D | ILE502 |
| D | PHE506 |
| D | MET523 |
| D | GLN535 |
| D | PHE538 |
| D | HOH805 |
| D | HOH941 |
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 | HIS326 | |
| B | HIS326 | |
| C | HIS326 | |
| D | HIS326 |
| 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 | HIS326 | |
| D | HIS326 | |
| D | ASN487 | |
| D | GLN535 | |
| A | ASN487 | |
| A | GLN535 | |
| B | HIS326 | |
| B | ASN487 | |
| B | GLN535 | |
| C | HIS326 | |
| C | ASN487 | |
| C | GLN535 |
| 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 | HIS330 | |
| B | HIS330 | |
| C | HIS330 | |
| D | HIS330 |
| 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 | HIS366 | |
| A | ASP484 | |
| B | HIS366 | |
| B | ASP484 | |
| C | HIS366 | |
| C | ASP484 | |
| D | HIS366 | |
| D | ASP484 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW |
| Chain | Residue | Details |
| A | ASP367 | |
| A | PHE538 | |
| B | ASP367 | |
| B | PHE538 | |
| C | ASP367 | |
| C | PHE538 | |
| D | ASP367 | |
| D | PHE538 |
| 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 | LYS251 | |
| B | LYS251 | |
| C | LYS251 | |
| D | LYS251 |
