3SL5
Crystal structure of the catalytic domain of PDE4D2 complexed with compound 10d
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 | 5 |
| Details | BINDING SITE FOR RESIDUE ZN A 438 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | HOH585 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 439 |
| Chain | Residue |
| A | ASP201 |
| A | HOH528 |
| A | HOH529 |
| A | HOH597 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE J25 A 1 |
| Chain | Residue |
| A | TYR159 |
| A | MET273 |
| A | ASN321 |
| A | PRO322 |
| A | TYR329 |
| A | PHE340 |
| A | MET357 |
| A | SER368 |
| A | GLN369 |
| A | PHE372 |
| A | ILE376 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 2 |
| Chain | Residue |
| A | LYS262 |
| A | ASP266 |
| B | HOH567 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE DMS A 3 |
| Chain | Residue |
| A | ASP140 |
| A | THR141 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 4 |
| Chain | Residue |
| A | THR186 |
| A | LEU188 |
| A | GLU189 |
| D | EDO4 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN B 438 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | ZN439 |
| B | HOH564 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN B 439 |
| Chain | Residue |
| B | ASP201 |
| B | ZN438 |
| B | HOH527 |
| B | HOH566 |
| B | HOH580 |
| B | HOH587 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE J25 B 1 |
| Chain | Residue |
| B | TYR159 |
| B | MET273 |
| B | LEU319 |
| B | ASN321 |
| B | PRO322 |
| B | TYR329 |
| B | THR333 |
| B | MET337 |
| B | PHE340 |
| B | MET357 |
| B | GLN369 |
| B | PHE372 |
| B | HOH591 |
| site_id | BC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 2 |
| Chain | Residue |
| B | GLU218 |
| C | LEU221 |
| site_id | BC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B 3 |
| Chain | Residue |
| B | HIS160 |
| B | HIS204 |
| B | GLY206 |
| B | VAL207 |
| B | GLU339 |
| B | PHE340 |
| B | GLN343 |
| site_id | BC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EPE C 5 |
| Chain | Residue |
| C | HIS105 |
| C | VAL106 |
| C | PHE107 |
| C | ARG108 |
| C | GLU111 |
| C | GLN327 |
| C | LEU328 |
| C | GLN331 |
| site_id | BC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE ZN C 438 |
| Chain | Residue |
| C | HIS164 |
| C | HIS200 |
| C | ASP201 |
| C | ASP318 |
| C | ZN439 |
| C | HOH523 |
| C | HOH556 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN C 439 |
| Chain | Residue |
| C | ASP201 |
| C | ZN438 |
| C | HOH520 |
| C | HOH523 |
| C | HOH564 |
| C | HOH581 |
| site_id | BC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE J25 C 1 |
| Chain | Residue |
| C | TYR159 |
| C | MET273 |
| C | ASN321 |
| C | TYR329 |
| C | TRP332 |
| C | THR333 |
| C | ILE336 |
| C | PHE340 |
| C | SER368 |
| C | GLN369 |
| C | PHE372 |
| C | ILE376 |
| C | HOH522 |
| site_id | BC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO C 2 |
| Chain | Residue |
| C | THR134 |
| C | PHE135 |
| C | LYS136 |
| C | ASN251 |
| C | GLN256 |
| B | HIS389 |
| B | PRO390 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 3 |
| Chain | Residue |
| B | GLU182 |
| C | LEU188 |
| C | LYS255 |
| C | SER259 |
| site_id | BC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO C 4 |
| Chain | Residue |
| C | GLU97 |
| C | GLU128 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 6 |
| Chain | Residue |
| C | ASP98 |
| C | LYS101 |
| C | TRP102 |
| C | GLY103 |
| C | HIS105 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 7 |
| Chain | Residue |
| C | ASP266 |
| C | LYS275 |
| C | GLN311 |
| site_id | CC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 2 |
| Chain | Residue |
| B | THR215 |
| B | SER217 |
| D | HIS152 |
| D | GLU243 |
| D | HOH527 |
| site_id | CC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 5 |
| Chain | Residue |
| C | GLN242 |
| D | ASN216 |
| D | LEU221 |
| site_id | CC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN D 438 |
| Chain | Residue |
| D | HIS164 |
| D | HIS200 |
| D | ASP201 |
| D | ASP318 |
| D | ZN439 |
| D | HOH606 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN D 439 |
| Chain | Residue |
| D | ASP201 |
| D | ZN438 |
| D | HOH532 |
| D | HOH542 |
| D | HOH625 |
| site_id | CC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE J25 D 1 |
| Chain | Residue |
| D | TYR159 |
| D | MET273 |
| D | LEU319 |
| D | ASN321 |
| D | PRO322 |
| D | TYR329 |
| D | MET357 |
| D | SER368 |
| D | GLN369 |
| D | PHE372 |
| D | ILE376 |
| D | HOH607 |
| site_id | CC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 3 |
| Chain | Residue |
| D | LEU181 |
| D | ALA183 |
| D | VAL184 |
| D | PHE185 |
| D | ILE190 |
| D | HOH596 |
| D | HOH619 |
| site_id | CC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 4 |
| Chain | Residue |
| A | EDO4 |
| A | LEU188 |
| A | LYS255 |
| A | GLN256 |
| D | GLU182 |
| site_id | DC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 6 |
| Chain | Residue |
| D | THR178 |
| D | ILE395 |
| D | HOH605 |
| site_id | DC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 8 |
| Chain | Residue |
| A | THR134 |
| A | ASN251 |
| A | GLN256 |
| D | PRO179 |
| D | ASP391 |
| site_id | DC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 7 |
| Chain | Residue |
| D | ASN115 |
| D | ARG116 |
| D | GLU150 |
| D | ASP151 |
| D | TYR153 |
| site_id | DC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO D 9 |
| Chain | Residue |
| D | ASN115 |
| D | HOH583 |
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 | HIS200-PHE211 |
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 | HIS160 | |
| B | HIS160 | |
| C | HIS160 | |
| D | HIS160 |
| 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 | HIS160 | |
| D | HIS160 | |
| D | ASN321 | |
| D | GLN369 | |
| A | ASN321 | |
| A | GLN369 | |
| B | HIS160 | |
| B | ASN321 | |
| B | GLN369 | |
| C | HIS160 | |
| C | ASN321 | |
| C | GLN369 |
| 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 | HIS164 | |
| B | HIS164 | |
| C | HIS164 | |
| D | HIS164 |
| 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 | HIS200 | |
| A | ASP318 | |
| B | HIS200 | |
| B | ASP318 | |
| C | HIS200 | |
| C | ASP318 | |
| D | HIS200 | |
| D | ASP318 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW |
| Chain | Residue | Details |
| A | ASP201 | |
| A | PHE372 | |
| B | ASP201 | |
| B | PHE372 | |
| C | ASP201 | |
| C | PHE372 | |
| D | ASP201 | |
| D | PHE372 |
| 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 | LYS85 | |
| B | LYS85 | |
| C | LYS85 | |
| D | LYS85 |
