4OGB
Crystal structure of the catalytic domain of PDE4D2 with compound 2
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 | 8 |
| Details | BINDING SITE FOR RESIDUE 2SR A 501 |
| Chain | Residue |
| A | HIS160 |
| A | MET273 |
| A | LEU319 |
| A | MET357 |
| A | SER368 |
| A | GLN369 |
| A | PHE372 |
| A | ILE376 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 502 |
| Chain | Residue |
| C | LYS239 |
| A | GLU218 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 503 |
| Chain | Residue |
| A | LEU132 |
| A | LYS136 |
| A | HOH628 |
| D | ASP394 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG A 504 |
| Chain | Residue |
| A | GLU150 |
| A | ASP151 |
| A | TYR153 |
| A | HOH640 |
| C | ARG346 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 505 |
| Chain | Residue |
| A | LYS255 |
| A | GLN256 |
| D | GLU182 |
| D | DMS504 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 506 |
| Chain | Residue |
| A | PHE238 |
| A | PHE249 |
| A | ARG257 |
| A | HOH609 |
| A | HOH631 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO A 507 |
| Chain | Residue |
| A | ASN278 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 508 |
| Chain | Residue |
| A | LYS239 |
| A | GLN242 |
| A | GLU243 |
| A | HOH608 |
| C | ASN216 |
| D | GLN242 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN A 509 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | HOH668 |
| A | HOH707 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN A 510 |
| Chain | Residue |
| A | ASP201 |
| A | HOH606 |
| A | HOH614 |
| A | HOH616 |
| A | HOH668 |
| A | HOH708 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE DMS A 511 |
| Chain | Residue |
| A | PRO138 |
| A | ASP140 |
| A | THR141 |
| A | HOH686 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 512 |
| Chain | Residue |
| A | LYS262 |
| A | ILE265 |
| A | ASP266 |
| A | HOH633 |
| B | HOH616 |
| site_id | BC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS A 513 |
| Chain | Residue |
| A | HIS105 |
| A | VAL106 |
| A | PHE107 |
| A | ARG108 |
| A | GLN327 |
| A | GLN331 |
| site_id | BC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 514 |
| Chain | Residue |
| A | HIS152 |
| A | GLU243 |
| C | SER217 |
| C | ARG350 |
| site_id | BC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE 2SR B 501 |
| Chain | Residue |
| B | HIS160 |
| B | MET273 |
| B | LEU319 |
| B | MET357 |
| B | SER368 |
| B | GLN369 |
| B | PHE372 |
| B | DMS510 |
| B | HOH613 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN B 502 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | HOH617 |
| B | HOH690 |
| site_id | BC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN B 503 |
| Chain | Residue |
| B | ASP201 |
| B | HOH603 |
| B | HOH606 |
| B | HOH609 |
| B | HOH617 |
| B | HOH689 |
| site_id | BC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 504 |
| Chain | Residue |
| B | SER208 |
| B | PHE340 |
| B | PRO356 |
| B | CYS358 |
| B | HOH692 |
| site_id | CC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 505 |
| Chain | Residue |
| B | PHE107 |
| B | GLN331 |
| B | ASP334 |
| B | ARG335 |
| site_id | CC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 506 |
| Chain | Residue |
| B | HOH625 |
| D | SER294 |
| D | SER295 |
| A | GLN258 |
| B | ASN214 |
| B | EDO507 |
| site_id | CC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 507 |
| Chain | Residue |
| B | PHE211 |
| B | ASN214 |
| B | GLU347 |
| B | MET352 |
| B | GLU353 |
| B | SER355 |
| B | EDO506 |
| B | HOH625 |
| site_id | CC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO B 508 |
| Chain | Residue |
| B | ALA183 |
| site_id | CC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 509 |
| Chain | Residue |
| B | LYS101 |
| B | TRP102 |
| B | GLY103 |
| B | LEU104 |
| B | VAL106 |
| B | ASP167 |
| B | GLN170 |
| B | LYS324 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE DMS B 510 |
| Chain | Residue |
| B | TYR159 |
| B | ASN321 |
| B | PRO322 |
| B | THR333 |
| B | PHE372 |
| B | 2SR501 |
| site_id | CC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO B 511 |
| Chain | Residue |
| B | ASP140 |
| site_id | CC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS B 512 |
| Chain | Residue |
| B | GLU349 |
| B | ARG350 |
| D | ASP140 |
| D | ILE143 |
| D | THR144 |
| site_id | CC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 501 |
| Chain | Residue |
| C | THR148 |
| C | HIS152 |
| C | GLU243 |
| site_id | DC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE 2SR C 502 |
| Chain | Residue |
| C | HIS160 |
| C | MET273 |
| C | LEU319 |
| C | MET357 |
| C | GLN369 |
| C | PHE372 |
| site_id | DC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO C 503 |
| Chain | Residue |
| C | ASN115 |
| C | ALA155 |
| C | ASN161 |
| C | ASN162 |
| C | ILE163 |
| C | ARG335 |
| site_id | DC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO C 504 |
| Chain | Residue |
| B | HIS389 |
| B | PRO390 |
| C | THR134 |
| C | PHE135 |
| C | ASN251 |
| C | GLN256 |
| site_id | DC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 505 |
| Chain | Residue |
| B | PRO179 |
| C | LEU188 |
| C | LYS255 |
| site_id | DC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EPE C 506 |
| Chain | Residue |
| C | HIS105 |
| C | VAL106 |
| C | PHE107 |
| C | ARG108 |
| C | GLU111 |
| C | GLN327 |
| C | LEU328 |
| C | GLN331 |
| site_id | DC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 507 |
| Chain | Residue |
| C | LYS262 |
| C | ASP266 |
| D | ASN224 |
| D | ASP225 |
| site_id | DC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 508 |
| Chain | Residue |
| C | ASP266 |
| C | LEU269 |
| C | LYS275 |
| C | GLN311 |
| site_id | DC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 509 |
| Chain | Residue |
| C | ASN115 |
| C | GLU150 |
| C | ASP151 |
| C | TYR153 |
| C | ASN162 |
| site_id | DC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN C 510 |
| Chain | Residue |
| C | HIS164 |
| C | HIS200 |
| C | ASP201 |
| C | ASP318 |
| C | HOH601 |
| C | HOH666 |
| site_id | EC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN C 511 |
| Chain | Residue |
| C | ASP201 |
| C | HOH602 |
| C | HOH613 |
| C | HOH664 |
| C | HOH665 |
| C | HOH666 |
| site_id | EC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 512 |
| Chain | Residue |
| C | LEU219 |
| C | MET222 |
| C | TYR223 |
| site_id | EC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO C 513 |
| Chain | Residue |
| C | LEU175 |
| C | THR178 |
| C | TRP384 |
| C | ASP391 |
| C | ALA392 |
| site_id | EC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 501 |
| Chain | Residue |
| B | PHE211 |
| B | THR215 |
| B | ARG350 |
| D | THR148 |
| D | HIS152 |
| D | GLU243 |
| D | HOH691 |
| site_id | EC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE 2SR D 502 |
| Chain | Residue |
| D | HIS160 |
| D | MET273 |
| D | LEU319 |
| D | PHE340 |
| D | MET357 |
| D | SER368 |
| D | GLN369 |
| D | PHE372 |
| D | ILE376 |
| site_id | EC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 503 |
| Chain | Residue |
| D | THR178 |
| D | TRP384 |
| D | VAL388 |
| D | ASP391 |
| D | PEG515 |
| D | PEG516 |
| D | HOH671 |
| site_id | EC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE DMS D 504 |
| Chain | Residue |
| A | EDO505 |
| D | SER177 |
| D | GLU182 |
| site_id | EC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO D 505 |
| Chain | Residue |
| D | VAL120 |
| D | HIS123 |
| site_id | EC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 506 |
| Chain | Residue |
| D | ASP266 |
| D | GLN311 |
| D | PEG507 |
| site_id | FC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG D 507 |
| Chain | Residue |
| C | ASP225 |
| C | HOH628 |
| D | LYS262 |
| D | ASP266 |
| D | EDO506 |
| D | HOH670 |
| site_id | FC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE DMS D 508 |
| Chain | Residue |
| D | GLU150 |
| D | ASP151 |
| D | TYR153 |
| D | ASN162 |
| D | EDO510 |
| site_id | FC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 509 |
| Chain | Residue |
| D | ASP266 |
| D | LYS275 |
| D | GLN311 |
| site_id | FC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO D 510 |
| Chain | Residue |
| D | ASN115 |
| D | ALA155 |
| D | ASN161 |
| D | ASN162 |
| D | ILE163 |
| D | DMS508 |
| site_id | FC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 511 |
| Chain | Residue |
| D | GLU128 |
| D | HIS173 |
| D | SER177 |
| site_id | FC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN D 512 |
| Chain | Residue |
| D | HIS164 |
| D | HIS200 |
| D | ASP201 |
| D | ASP318 |
| D | HOH711 |
| D | HOH712 |
| site_id | FC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN D 513 |
| Chain | Residue |
| D | ASP201 |
| D | HOH606 |
| D | HOH623 |
| D | HOH662 |
| D | HOH711 |
| D | HOH713 |
| site_id | FC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO D 514 |
| Chain | Residue |
| A | THR134 |
| A | ASN251 |
| A | GLN256 |
| D | PRO179 |
| D | ASP391 |
| D | HOH717 |
| site_id | FC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG D 515 |
| Chain | Residue |
| A | THR134 |
| A | HOH661 |
| D | ASP391 |
| D | EDO503 |
| D | PEG516 |
| D | HOH717 |
| site_id | GC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE PEG D 516 |
| Chain | Residue |
| D | LYS101 |
| D | TRP102 |
| D | VAL174 |
| D | ASP394 |
| D | ILE395 |
| D | EDO503 |
| D | PEG515 |
| D | HOH615 |
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 |
