5LBO
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001
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 1001 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | HOH1108 |
| A | HOH1124 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 1002 |
| Chain | Residue |
| A | HOH1134 |
| A | HOH1169 |
| A | HOH1191 |
| A | ASP201 |
| A | HOH1108 |
| A | HOH1110 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 1003 |
| Chain | Residue |
| A | SER208 |
| A | PRO356 |
| A | HOH1125 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 1004 |
| Chain | Residue |
| A | ASN115 |
| A | ALA155 |
| A | ASN162 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 1005 |
| Chain | Residue |
| A | THR186 |
| A | GLU189 |
| A | SER259 |
| A | HOH1123 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 1006 |
| Chain | Residue |
| A | LYS262 |
| A | ASP266 |
| A | HOH1107 |
| A | HOH1109 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 1007 |
| Chain | Residue |
| A | VAL174 |
| A | THR178 |
| A | ASP391 |
| A | ILE395 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 1008 |
| Chain | Residue |
| A | GLU218 |
| C | LYS239 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 1009 |
| Chain | Residue |
| A | ASP266 |
| A | LEU269 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue DTT A 1010 |
| Chain | Residue |
| A | THR134 |
| A | ASP187 |
| site_id | AD2 |
| Number of Residues | 12 |
| Details | binding site for residue 6M5 A 1011 |
| Chain | Residue |
| A | MET273 |
| A | LEU319 |
| A | ASN321 |
| A | ILE336 |
| A | MET357 |
| A | SER368 |
| A | GLN369 |
| A | GLY371 |
| A | PHE372 |
| A | TYR375 |
| A | HOH1153 |
| A | HOH1192 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 1012 |
| Chain | Residue |
| A | HIS152 |
| A | GLU243 |
| C | THR215 |
| C | SER217 |
| C | ARG350 |
| site_id | AD4 |
| Number of Residues | 9 |
| Details | binding site for residue DTT A 1013 |
| Chain | Residue |
| A | GLU150 |
| A | ASP151 |
| A | TYR153 |
| A | HIS154 |
| A | ALA155 |
| A | HOH1156 |
| C | ASP156 |
| C | HOH1158 |
| C | HOH1173 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 1001 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | HOH1108 |
| B | HOH1149 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 1002 |
| Chain | Residue |
| B | ASP201 |
| B | HOH1108 |
| B | HOH1116 |
| B | HOH1154 |
| B | HOH1162 |
| B | HOH1182 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 1003 |
| Chain | Residue |
| B | SER208 |
| B | PHE340 |
| B | PRO356 |
| B | CYS358 |
| B | HOH1120 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1004 |
| Chain | Residue |
| B | ASN115 |
| B | ALA155 |
| B | ASN162 |
| B | ILE163 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 1005 |
| Chain | Residue |
| A | ASN224 |
| A | ASP225 |
| B | LYS262 |
| B | ASP266 |
| site_id | AE1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 1006 |
| Chain | Residue |
| B | VAL292 |
| B | HOH1143 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1007 |
| Chain | Residue |
| B | PHE211 |
| B | ASN214 |
| B | GLU347 |
| B | MET352 |
| B | GLU353 |
| B | SER355 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 1008 |
| Chain | Residue |
| D | HIS152 |
| D | GLU243 |
| B | PHE211 |
| B | THR215 |
| B | ARG346 |
| B | ARG350 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 1009 |
| Chain | Residue |
| B | GLU349 |
| B | ARG350 |
| D | ILE143 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue EPE B 1010 |
| Chain | Residue |
| B | ASP140 |
| B | GLN250 |
| B | HOH1102 |
| C | THR253 |
| C | LYS254 |
| site_id | AE6 |
| Number of Residues | 10 |
| Details | binding site for residue 6M5 B 1011 |
| Chain | Residue |
| B | MET273 |
| B | LEU319 |
| B | ASN321 |
| B | ILE336 |
| B | MET357 |
| B | SER368 |
| B | GLN369 |
| B | PHE372 |
| B | TYR375 |
| B | HOH1156 |
| site_id | AE7 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 1001 |
| Chain | Residue |
| C | HIS164 |
| C | HIS200 |
| C | ASP201 |
| C | ASP318 |
| C | HOH1105 |
| C | HOH1126 |
| site_id | AE8 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 1002 |
| Chain | Residue |
| C | ASP201 |
| C | HOH1105 |
| C | HOH1114 |
| C | HOH1123 |
| C | HOH1144 |
| C | HOH1167 |
| site_id | AE9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 1003 |
| Chain | Residue |
| C | SER208 |
| C | PRO356 |
| C | HOH1107 |
| C | HOH1174 |
| site_id | AF1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 1004 |
| Chain | Residue |
| C | ARG257 |
| C | ARG261 |
| site_id | AF2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 1005 |
| Chain | Residue |
| C | LYS255 |
| C | SER259 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 1006 |
| Chain | Residue |
| C | THR178 |
| C | TRP384 |
| C | ASP391 |
| C | ILE395 |
| site_id | AF4 |
| Number of Residues | 8 |
| Details | binding site for residue EPE C 1007 |
| Chain | Residue |
| C | HIS105 |
| C | VAL106 |
| C | PHE107 |
| C | ARG108 |
| C | GLU111 |
| C | GLN327 |
| C | LEU328 |
| C | GLN331 |
| site_id | AF5 |
| Number of Residues | 11 |
| Details | binding site for residue 6M5 C 1008 |
| Chain | Residue |
| C | MET273 |
| C | LEU319 |
| C | ASN321 |
| C | ILE336 |
| C | MET357 |
| C | SER368 |
| C | GLN369 |
| C | PHE372 |
| C | TYR375 |
| C | HOH1135 |
| C | HOH1174 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 1001 |
| Chain | Residue |
| D | HIS164 |
| D | HIS200 |
| D | ASP201 |
| D | ASP318 |
| D | HOH1122 |
| D | HOH1174 |
| site_id | AF7 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 1002 |
| Chain | Residue |
| D | ASP201 |
| D | HOH1122 |
| D | HOH1124 |
| D | HOH1165 |
| D | HOH1173 |
| D | HOH1206 |
| site_id | AF8 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 1003 |
| Chain | Residue |
| D | SER294 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 1004 |
| Chain | Residue |
| D | SER208 |
| D | SER355 |
| D | PRO356 |
| D | CYS358 |
| D | HOH1134 |
| site_id | AG1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 1005 |
| Chain | Residue |
| D | LYS262 |
| D | ASP266 |
| D | HOH1114 |
| site_id | AG2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO D 1006 |
| Chain | Residue |
| D | ASN115 |
| D | ALA155 |
| D | ASN161 |
| D | ASN162 |
| D | ILE163 |
| D | ARG335 |
| D | DTT1014 |
| D | HOH1179 |
| site_id | AG3 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 1007 |
| Chain | Residue |
| D | HOH1166 |
| site_id | AG4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 1008 |
| Chain | Residue |
| D | THR186 |
| D | LEU188 |
| D | SER259 |
| D | EDO1010 |
| D | HOH1161 |
| site_id | AG5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 1009 |
| Chain | Residue |
| D | THR134 |
| D | LYS136 |
| D | ASN251 |
| D | GLN256 |
| site_id | AG6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 1010 |
| Chain | Residue |
| D | SER259 |
| D | TYR303 |
| D | EDO1008 |
| site_id | AG7 |
| Number of Residues | 1 |
| Details | binding site for residue EDO D 1011 |
| Chain | Residue |
| D | GLU182 |
| site_id | AG8 |
| Number of Residues | 7 |
| Details | binding site for residue PEG D 1012 |
| Chain | Residue |
| D | VAL174 |
| D | LEU175 |
| D | THR178 |
| D | TRP384 |
| D | VAL388 |
| D | PEG1013 |
| D | HOH1125 |
| site_id | AG9 |
| Number of Residues | 3 |
| Details | binding site for residue PEG D 1013 |
| Chain | Residue |
| D | PRO179 |
| D | ASP391 |
| D | PEG1012 |
| site_id | AH1 |
| Number of Residues | 12 |
| Details | binding site for residue DTT D 1014 |
| Chain | Residue |
| B | ASP156 |
| B | HOH1165 |
| D | ASN115 |
| D | ARG116 |
| D | GLU150 |
| D | ASP151 |
| D | TYR153 |
| D | HIS154 |
| D | ALA155 |
| D | EDO1006 |
| D | HOH1103 |
| D | HOH1205 |
| site_id | AH2 |
| Number of Residues | 10 |
| Details | binding site for residue 6M5 D 1015 |
| Chain | Residue |
| D | MET273 |
| D | LEU319 |
| D | ASN321 |
| D | ILE336 |
| D | MET357 |
| D | SER368 |
| D | GLN369 |
| D | PHE372 |
| D | TYR375 |
| D | HOH1137 |
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 |
