6BOJ
Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004
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 | HOH818 |
| A | HOH963 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 702 |
| Chain | Residue |
| A | HOH899 |
| A | HOH938 |
| A | HOH1022 |
| A | ASP367 |
| A | HOH818 |
| A | HOH881 |
| site_id | AC3 |
| Number of Residues | 14 |
| Details | binding site for residue E31 A 703 |
| Chain | Residue |
| A | HIS326 |
| A | SER374 |
| A | ASN487 |
| A | TYR495 |
| A | ILE502 |
| A | PHE506 |
| A | GLN535 |
| A | PHE538 |
| A | PHE599 |
| A | ILE600 |
| A | HOH869 |
| A | HOH923 |
| A | HOH925 |
| A | HOH942 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue ZN A 704 |
| Chain | Residue |
| A | HIS318 |
| A | HOH810 |
| A | HOH1047 |
| A | HOH1061 |
| C | HOH829 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue CL A 705 |
| Chain | Residue |
| A | HIS271 |
| A | PHE273 |
| A | ARG274 |
| A | HOH1045 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 701 |
| Chain | Residue |
| B | HIS330 |
| B | HIS366 |
| B | ASP367 |
| B | ASP484 |
| B | HOH1031 |
| B | HOH1131 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 702 |
| Chain | Residue |
| B | ASP367 |
| B | HOH1031 |
| B | HOH1063 |
| B | HOH1121 |
| B | HOH1148 |
| B | HOH1193 |
| site_id | AC8 |
| Number of Residues | 14 |
| Details | binding site for residue E31 B 703 |
| Chain | Residue |
| B | HIS326 |
| B | ASN487 |
| B | TYR495 |
| B | THR499 |
| B | ILE502 |
| B | PHE506 |
| B | GLN535 |
| B | PHE538 |
| B | PHE599 |
| B | ILE600 |
| B | HOH1046 |
| B | HOH1104 |
| B | HOH1117 |
| B | HOH1162 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue CL B 704 |
| Chain | Residue |
| B | HIS271 |
| B | PHE273 |
| B | ARG274 |
| B | HOH1032 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue MPD B 705 |
| Chain | Residue |
| B | LEU378 |
| B | SER383 |
| B | ARG512 |
| B | HOH1141 |
| B | HOH1201 |
| D | HOH951 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 701 |
| Chain | Residue |
| C | HIS330 |
| C | HIS366 |
| C | ASP367 |
| C | ASP484 |
| C | HOH840 |
| C | HOH974 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 702 |
| Chain | Residue |
| C | ASP367 |
| C | HOH840 |
| C | HOH868 |
| C | HOH900 |
| C | HOH954 |
| C | HOH1034 |
| site_id | AD4 |
| Number of Residues | 13 |
| Details | binding site for residue E31 C 703 |
| Chain | Residue |
| C | HIS326 |
| C | ASN487 |
| C | TYR495 |
| C | ILE502 |
| C | PHE506 |
| C | GLN535 |
| C | PHE538 |
| C | PHE599 |
| C | ILE600 |
| C | HOH858 |
| C | HOH896 |
| C | HOH926 |
| C | HOH933 |
| site_id | AD5 |
| Number of Residues | 3 |
| Details | binding site for residue CL C 704 |
| Chain | Residue |
| C | HIS271 |
| C | PHE273 |
| C | ARG274 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue MPD C 705 |
| Chain | Residue |
| C | ARG512 |
| C | HOH947 |
| 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 | HOH829 |
| D | HOH937 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 702 |
| Chain | Residue |
| D | ASP367 |
| D | HOH829 |
| D | HOH864 |
| D | HOH889 |
| D | HOH944 |
| D | HOH967 |
| site_id | AD9 |
| Number of Residues | 10 |
| Details | binding site for residue E31 D 703 |
| Chain | Residue |
| D | HIS326 |
| D | ASN487 |
| D | ILE502 |
| D | PHE506 |
| D | GLN535 |
| D | PHE538 |
| D | PHE599 |
| D | HOH892 |
| D | HOH901 |
| D | HOH934 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue ZN D 704 |
| Chain | Residue |
| B | HOH1008 |
| D | HIS318 |
| D | HOH821 |
| D | HOH1000 |
| D | HOH1011 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue CL D 705 |
| Chain | Residue |
| D | HIS271 |
| D | PHE273 |
| D | ARG274 |
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 | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P14270 |
| Chain | Residue | Details |
| A | LEU297 | |
| B | LEU297 | |
| C | LEU297 | |
| D | LEU297 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | GLU454 | |
| A | LYS456 | |
| B | GLU454 | |
| B | LYS456 | |
| C | GLU454 | |
| C | LYS456 | |
| D | GLU454 | |
| D | LYS456 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | MET503 | |
| A | SER530 | |
| B | MET503 | |
| B | SER530 | |
| C | MET503 | |
| C | SER530 | |
| D | MET503 | |
| D | SER530 |
| site_id | SWS_FT_FI9 |
| 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 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P14646 |
| Chain | Residue | Details |
| A | ALA579 | |
| A | ALA581 | |
| B | ALA579 | |
| B | ALA581 | |
| C | ALA579 | |
| C | ALA581 | |
| D | ALA579 | |
| D | ALA581 |
