1TB7
Catalytic Domain Of Human Phosphodiesterase 4D In Complex With AMP
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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE ZN A 1001 |
| Chain | Residue |
| A | HIS164 |
| A | HIS200 |
| A | ASP201 |
| A | ASP318 |
| A | MG1002 |
| A | AMP1003 |
| A | HOH1190 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG A 1002 |
| Chain | Residue |
| A | AMP1003 |
| A | HOH1187 |
| A | HOH1188 |
| A | HOH1189 |
| A | HOH1190 |
| A | ASP201 |
| A | ZN1001 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE ZN B 1001 |
| Chain | Residue |
| B | HIS164 |
| B | HIS200 |
| B | ASP201 |
| B | ASP318 |
| B | MG1002 |
| B | AMP1003 |
| B | HOH1175 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG B 1002 |
| Chain | Residue |
| B | ASP201 |
| B | ZN1001 |
| B | AMP1003 |
| B | HOH1172 |
| B | HOH1173 |
| B | HOH1174 |
| B | HOH1175 |
| site_id | AC5 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE AMP B 1003 |
| Chain | Residue |
| B | HIS160 |
| B | HIS164 |
| B | ASP201 |
| B | ASP318 |
| B | LEU319 |
| B | ASN321 |
| B | GLN369 |
| B | PHE372 |
| B | EDO543 |
| B | ZN1001 |
| B | MG1002 |
| B | HOH1004 |
| B | HOH1027 |
| B | HOH1104 |
| B | HOH1174 |
| B | HOH1175 |
| site_id | AC6 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE AMP A 1003 |
| Chain | Residue |
| A | HIS160 |
| A | HIS164 |
| A | ASP201 |
| A | ASP318 |
| A | LEU319 |
| A | ASN321 |
| A | GLN369 |
| A | PHE372 |
| A | EDO523 |
| A | ZN1001 |
| A | MG1002 |
| A | HOH1005 |
| A | HOH1053 |
| A | HOH1057 |
| A | HOH1105 |
| A | HOH1187 |
| A | HOH1189 |
| A | HOH1190 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 501 |
| Chain | Residue |
| B | GLU366 |
| B | EDO503 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 502 |
| Chain | Residue |
| A | LYS262 |
| A | ILE265 |
| A | ASP266 |
| A | HOH1021 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 503 |
| Chain | Residue |
| B | ARG330 |
| B | THR333 |
| B | ASP334 |
| B | TYR406 |
| B | EDO501 |
| B | HOH1165 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 508 |
| Chain | Residue |
| B | SER208 |
| B | PHE340 |
| B | PRO356 |
| B | HOH1059 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 509 |
| Chain | Residue |
| B | SER259 |
| B | HOH1056 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 515 |
| Chain | Residue |
| A | ASN115 |
| A | ALA155 |
| A | ASN162 |
| A | HOH1064 |
| A | HOH1103 |
| site_id | BC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 516 |
| Chain | Residue |
| A | THR178 |
| A | TRP384 |
| A | VAL388 |
| A | ASP391 |
| A | ALA392 |
| A | ILE395 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 517 |
| Chain | Residue |
| B | PHE238 |
| B | ARG257 |
| B | ARG261 |
| B | HOH1084 |
| B | HOH1093 |
| site_id | BC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 519 |
| Chain | Residue |
| A | ALA183 |
| A | VAL184 |
| A | PHE185 |
| site_id | BC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 520 |
| Chain | Residue |
| A | ARG257 |
| A | ARG261 |
| A | HOH1146 |
| site_id | BC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE EDO A 521 |
| Chain | Residue |
| A | HIS160 |
| A | GLY206 |
| A | VAL207 |
| A | SER208 |
| A | GLU339 |
| A | PHE340 |
| A | GLN343 |
| A | EDO522 |
| A | HOH1057 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 522 |
| Chain | Residue |
| A | SER208 |
| A | PRO356 |
| A | CYS358 |
| A | EDO521 |
| site_id | CC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE EDO A 523 |
| Chain | Residue |
| A | ASN209 |
| A | LEU229 |
| A | GLU230 |
| A | ASP272 |
| A | MET273 |
| A | AMP1003 |
| A | HOH1053 |
| A | HOH1056 |
| A | HOH1137 |
| A | HOH1187 |
| site_id | CC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 524 |
| Chain | Residue |
| A | HOH1032 |
| B | GLU218 |
| site_id | CC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 525 |
| Chain | Residue |
| A | ASN224 |
| B | LYS262 |
| B | ILE265 |
| B | ASP266 |
| B | HOH1011 |
| B | HOH1087 |
| site_id | CC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B 526 |
| Chain | Residue |
| A | GLN407 |
| B | GLU150 |
| B | ASP151 |
| B | TYR153 |
| B | ASN162 |
| B | EDO534 |
| B | HOH1075 |
| site_id | CC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 533 |
| Chain | Residue |
| A | HIS154 |
| A | ASP203 |
| A | PRO205 |
| A | LEU219 |
| site_id | CC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B 534 |
| Chain | Residue |
| B | ASN115 |
| B | ALA155 |
| B | ASN162 |
| B | ILE163 |
| B | EDO526 |
| B | HOH1075 |
| B | HOH1164 |
| site_id | CC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 535 |
| Chain | Residue |
| B | ASN209 |
| B | GLU230 |
| B | MET273 |
| B | EDO543 |
| B | HOH1027 |
| site_id | CC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 536 |
| Chain | Residue |
| A | ARG330 |
| A | GLU366 |
| A | TRP405 |
| A | TYR406 |
| A | HOH1088 |
| B | PRO411 |
| site_id | CC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 537 |
| Chain | Residue |
| A | PRO325 |
| A | GLN327 |
| A | HOH1055 |
| B | TRP405 |
| B | HOH1076 |
| site_id | DC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 538 |
| Chain | Residue |
| A | THR186 |
| A | LEU188 |
| A | GLU189 |
| A | SER259 |
| A | MET263 |
| A | HOH1120 |
| site_id | DC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 539 |
| Chain | Residue |
| A | ARG116 |
| A | MET147 |
| A | THR148 |
| A | ASP151 |
| site_id | DC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 540 |
| Chain | Residue |
| A | ASP334 |
| A | MET337 |
| A | GLU338 |
| A | PHE341 |
| A | HOH1111 |
| site_id | DC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 541 |
| Chain | Residue |
| B | ASP266 |
| B | ILE307 |
| B | GLN311 |
| B | EDO542 |
| B | HOH1106 |
| site_id | DC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B 542 |
| Chain | Residue |
| B | ASP266 |
| B | LEU269 |
| B | LYS275 |
| B | GLN311 |
| B | EDO541 |
| site_id | DC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE EDO B 543 |
| Chain | Residue |
| B | HIS160 |
| B | HIS204 |
| B | GLY206 |
| B | VAL207 |
| B | SER208 |
| B | GLU339 |
| B | EDO535 |
| B | AMP1003 |
| B | HOH1027 |
| B | HOH1059 |
| site_id | DC7 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE B3P A 601 |
| Chain | Residue |
| A | LYS94 |
| A | GLU95 |
| A | GLU97 |
| A | ASP98 |
| A | HIS105 |
| A | ARG108 |
| A | HOH1147 |
| B | ASP394 |
| B | ASP397 |
| B | ASP401 |
| B | HOH1123 |
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 | 2 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"Q07343","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15260978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15576036","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17582435","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TB7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TBB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XON","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XOR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2PW3","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"14609333","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PTW","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
