3SL6
Crystal structure of the catalytic domain of PDE4D2 with compound 12c
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 10 |
| Chain | Residue |
| A | ZN11 |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | HOH452 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN A 11 |
| Chain | Residue |
| A | HOH449 |
| A | HOH450 |
| A | ZN10 |
| A | ASP201 |
| A | HOH448 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 2 |
| Chain | Residue |
| A | GLU218 |
| C | LYS239 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 4 |
| Chain | Residue |
| A | THR134 |
| A | LYS136 |
| D | EDO7 |
| D | PRO179 |
| D | ASP391 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 5 |
| Chain | Residue |
| A | LEU175 |
| A | THR178 |
| A | TRP384 |
| A | ASP391 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 6 |
| Chain | Residue |
| A | ASN115 |
| A | ARG116 |
| A | GLU150 |
| A | ASP151 |
| A | TYR153 |
| A | ASN162 |
| A | HOH453 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 7 |
| Chain | Residue |
| A | ASP156 |
| A | VAL157 |
| A | ALA158 |
| A | ARG346 |
| A | HOH462 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 8 |
| Chain | Residue |
| A | ASN278 |
| A | LEU279 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 9 |
| Chain | Residue |
| A | HOH26 |
| A | HOH64 |
| A | PHE238 |
| A | PHE249 |
| A | ARG257 |
| A | ARG261 |
| site_id | BC1 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE JN8 A 440 |
| Chain | Residue |
| A | TYR159 |
| A | MET273 |
| A | LEU319 |
| A | ASN321 |
| A | PRO322 |
| A | TYR329 |
| A | ILE336 |
| A | MET337 |
| A | PHE340 |
| A | MET357 |
| A | SER368 |
| A | GLN369 |
| A | PHE372 |
| A | ILE376 |
| A | HOH451 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 441 |
| Chain | Residue |
| A | LYS262 |
| A | ASP266 |
| A | HOH446 |
| B | HOH452 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 442 |
| Chain | Residue |
| A | HIS152 |
| A | GLU243 |
| C | ARG350 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN B 7 |
| Chain | Residue |
| B | ZN8 |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN B 8 |
| Chain | Residue |
| B | ZN7 |
| B | ASP201 |
| B | HOH470 |
| B | HOH471 |
| B | HOH472 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 4 |
| Chain | Residue |
| B | ASN115 |
| B | ARG116 |
| B | GLU150 |
| B | ASP151 |
| B | TYR153 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 5 |
| Chain | Residue |
| B | LEU176 |
| B | SER177 |
| B | THR178 |
| B | GLU182 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 6 |
| Chain | Residue |
| B | ASP374 |
| B | HIS378 |
| B | PRO379 |
| B | GLU382 |
| site_id | BC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE JN8 B 440 |
| Chain | Residue |
| B | HOH443 |
| B | TYR159 |
| B | MET273 |
| B | LEU319 |
| B | ASN321 |
| B | THR333 |
| B | ILE336 |
| B | PHE340 |
| B | MET357 |
| B | CYS358 |
| B | SER368 |
| B | GLN369 |
| B | PHE372 |
| site_id | CC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS B 14 |
| Chain | Residue |
| B | GLU95 |
| B | ASP98 |
| B | GLY103 |
| B | HIS105 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 3 |
| Chain | Residue |
| A | ARG350 |
| C | HIS152 |
| C | GLU243 |
| site_id | CC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 10 |
| Chain | Residue |
| C | ZN11 |
| C | ASP201 |
| C | HOH462 |
| C | HOH464 |
| site_id | CC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN C 11 |
| Chain | Residue |
| C | ZN10 |
| C | HIS164 |
| C | HIS200 |
| C | ASP201 |
| C | ASP318 |
| C | HOH467 |
| site_id | CC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EPE C 2 |
| Chain | Residue |
| C | HIS105 |
| C | PHE107 |
| C | ARG108 |
| C | GLU111 |
| C | GLN327 |
| C | LEU328 |
| C | GLN331 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 440 |
| Chain | Residue |
| C | LEU175 |
| C | THR178 |
| C | TRP384 |
| C | ASP391 |
| C | ALA392 |
| site_id | CC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO C 4 |
| Chain | Residue |
| B | HIS389 |
| B | PRO390 |
| C | THR134 |
| C | PHE135 |
| C | LYS136 |
| C | ASN251 |
| C | GLN256 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 5 |
| Chain | Residue |
| C | GLU150 |
| C | ASP151 |
| C | TYR153 |
| C | ALA155 |
| site_id | CC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 7 |
| Chain | Residue |
| B | LYS290 |
| B | GLY296 |
| C | THR253 |
| C | LYS254 |
| C | LYS255 |
| site_id | DC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 8 |
| Chain | Residue |
| C | LEU234 |
| C | PHE238 |
| C | ARG261 |
| D | LEU221 |
| D | ASN224 |
| site_id | DC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 9 |
| Chain | Residue |
| C | LYS262 |
| C | ASP266 |
| D | ASN224 |
| D | ASP225 |
| site_id | DC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE JN8 C 441 |
| Chain | Residue |
| C | TYR159 |
| C | LEU319 |
| C | ASN321 |
| C | THR333 |
| C | ILE336 |
| C | PHE340 |
| C | CYS358 |
| C | GLN369 |
| C | PHE372 |
| C | HOH463 |
| site_id | DC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 3 |
| Chain | Residue |
| B | THR215 |
| B | ARG350 |
| D | THR148 |
| D | HIS152 |
| D | GLU243 |
| site_id | DC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN D 12 |
| Chain | Residue |
| D | ZN13 |
| D | ASP201 |
| D | HOH442 |
| D | HOH448 |
| D | HOH450 |
| site_id | DC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN D 13 |
| Chain | Residue |
| D | ZN12 |
| D | HIS164 |
| D | HIS200 |
| D | ASP201 |
| D | ASP318 |
| site_id | DC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 2 |
| Chain | Residue |
| A | LEU188 |
| A | LYS255 |
| A | GLN256 |
| A | SER259 |
| D | GLU182 |
| site_id | DC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 440 |
| Chain | Residue |
| D | EDO8 |
| D | LEU175 |
| D | THR178 |
| D | TRP384 |
| D | ASP391 |
| D | ILE395 |
| D | HOH456 |
| site_id | DC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO D 4 |
| Chain | Residue |
| D | THR186 |
| D | ASP187 |
| D | LEU188 |
| D | GLN256 |
| site_id | EC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO D 5 |
| Chain | Residue |
| D | HIS123 |
| site_id | EC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO D 6 |
| Chain | Residue |
| C | ASN224 |
| C | SER226 |
| D | EDO9 |
| D | LYS262 |
| D | ILE265 |
| D | ASP266 |
| site_id | EC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 7 |
| Chain | Residue |
| A | EDO4 |
| A | THR134 |
| A | PHE135 |
| A | ASN251 |
| A | GLN256 |
| D | PRO179 |
| D | ASP391 |
| site_id | EC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 8 |
| Chain | Residue |
| D | TRP102 |
| D | EDO440 |
| D | HOH481 |
| site_id | EC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 9 |
| Chain | Residue |
| C | HOH14 |
| C | HOH42 |
| C | ASP225 |
| D | EDO6 |
| D | GLN258 |
| D | ARG261 |
| D | LYS262 |
| site_id | EC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO D 10 |
| Chain | Residue |
| D | PRO325 |
| D | LEU326 |
| D | THR398 |
| D | ASN402 |
| site_id | EC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO D 11 |
| Chain | Residue |
| D | ASP156 |
| D | VAL157 |
| D | ALA158 |
| D | GLU339 |
| site_id | EC8 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE JN8 D 15 |
| Chain | Residue |
| D | TYR159 |
| D | MET273 |
| D | LEU319 |
| D | ASN321 |
| D | PRO322 |
| D | THR333 |
| D | ILE336 |
| D | PHE340 |
| D | MET357 |
| D | SER368 |
| D | GLN369 |
| D | PHE372 |
| D | HOH474 |
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 |
