3G58
Crystal structure of human phosphodiesterase 4d with d155988/pmnpq
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 624 |
| Chain | Residue |
| A | HIS330 |
| A | HIS366 |
| A | ASP367 |
| A | ASP484 |
| A | HOH792 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 625 |
| Chain | Residue |
| A | HOH792 |
| A | HOH1105 |
| A | ASP367 |
| A | HOH672 |
| A | HOH756 |
| A | HOH776 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1 |
| Chain | Residue |
| A | HIS271 |
| A | VAL272 |
| A | PHE273 |
| A | ARG274 |
| A | LEU494 |
| A | GLN497 |
| A | HOH939 |
| site_id | AC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE 988 A 901 |
| Chain | Residue |
| A | ASN487 |
| A | THR499 |
| A | ILE502 |
| A | PHE506 |
| A | SER534 |
| A | GLN535 |
| A | PHE538 |
| A | HOH679 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 6 |
| Chain | Residue |
| A | HOH193 |
| A | HIS318 |
| A | GLU409 |
| C | THR381 |
| C | SER383 |
| C | ARG516 |
| C | HOH941 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 7 |
| Chain | Residue |
| A | HOH37 |
| A | PHE404 |
| A | ARG423 |
| A | ARG427 |
| A | HOH651 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A 9 |
| Chain | Residue |
| A | SER374 |
| A | PRO522 |
| A | CYS524 |
| A | HOH679 |
| A | HOH697 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A 12 |
| Chain | Residue |
| A | HOH99 |
| A | LYS428 |
| A | ASP432 |
| B | HOH216 |
| B | SER392 |
| B | HOH751 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN B 624 |
| Chain | Residue |
| B | HIS330 |
| B | HIS366 |
| B | ASP367 |
| B | ASP484 |
| B | HOH876 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 625 |
| Chain | Residue |
| B | ASP367 |
| B | HOH639 |
| B | HOH728 |
| B | HOH758 |
| B | HOH760 |
| B | HOH876 |
| site_id | BC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE 988 B 902 |
| Chain | Residue |
| B | MET439 |
| B | ASN487 |
| B | THR499 |
| B | ILE502 |
| B | MET523 |
| B | SER534 |
| B | GLN535 |
| B | PHE538 |
| B | HOH697 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 3 |
| Chain | Residue |
| B | HOH88 |
| B | THR314 |
| B | HIS318 |
| B | GLU409 |
| B | HOH1033 |
| D | THR381 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 8 |
| Chain | Residue |
| B | HOH70 |
| B | LYS428 |
| B | ASP432 |
| B | HOH689 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B 10 |
| Chain | Residue |
| B | HIS271 |
| B | PHE273 |
| B | ARG274 |
| B | GLN493 |
| B | LEU494 |
| B | GLN497 |
| site_id | BC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 17 |
| Chain | Residue |
| B | SER374 |
| B | PRO522 |
| B | HOH697 |
| B | HOH774 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN C 624 |
| Chain | Residue |
| C | HOH230 |
| C | HIS330 |
| C | HIS366 |
| C | ASP367 |
| C | ASP484 |
| C | HOH1089 |
| site_id | BC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 625 |
| Chain | Residue |
| C | HOH733 |
| C | HOH1089 |
| C | ASP367 |
| C | HOH635 |
| C | HOH682 |
| C | HOH725 |
| site_id | BC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE 988 C 903 |
| Chain | Residue |
| C | ASN487 |
| C | THR499 |
| C | ILE502 |
| C | MET523 |
| C | GLN535 |
| C | PHE538 |
| C | HOH1002 |
| site_id | CC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 5 |
| Chain | Residue |
| C | LYS428 |
| C | ASP432 |
| C | HOH640 |
| D | HOH717 |
| site_id | CC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO C 13 |
| Chain | Residue |
| C | HIS271 |
| C | VAL272 |
| C | PHE273 |
| C | ARG274 |
| C | GLN493 |
| C | LEU494 |
| C | GLN497 |
| site_id | CC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO C 16 |
| Chain | Residue |
| A | THR381 |
| A | ARG516 |
| C | THR314 |
| C | HIS318 |
| C | GLU409 |
| C | HOH666 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 18 |
| Chain | Residue |
| C | HOH121 |
| C | PHE404 |
| C | ARG423 |
| C | ARG427 |
| site_id | CC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN D 624 |
| Chain | Residue |
| D | HIS330 |
| D | HIS366 |
| D | ASP367 |
| D | ASP484 |
| D | HOH852 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 625 |
| Chain | Residue |
| D | ASP367 |
| D | HOH630 |
| D | HOH722 |
| D | HOH724 |
| D | HOH852 |
| D | HOH1023 |
| site_id | CC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE 988 D 904 |
| Chain | Residue |
| D | MET439 |
| D | ASN487 |
| D | THR499 |
| D | ILE502 |
| D | PHE506 |
| D | MET523 |
| D | GLN535 |
| D | PHE538 |
| D | THR595 |
| D | PHE598 |
| D | GLN599 |
| D | HOH873 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO D 2 |
| Chain | Residue |
| C | HOH66 |
| C | HOH809 |
| D | LYS428 |
| D | ASP432 |
| site_id | CC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 4 |
| Chain | Residue |
| D | SER374 |
| D | PRO522 |
| D | CYS524 |
| D | PHE598 |
| D | GLU601 |
| D | HOH654 |
| D | HOH873 |
| site_id | DC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 11 |
| Chain | Residue |
| D | HIS271 |
| D | PHE273 |
| D | ARG274 |
| D | GLN493 |
| D | LEU494 |
| D | GLN497 |
| D | HOH1109 |
| site_id | DC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 14 |
| Chain | Residue |
| D | ARG295 |
| D | ASP353 |
| D | ILE356 |
| site_id | DC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 15 |
| Chain | Residue |
| D | HOH229 |
| D | PHE404 |
| D | ARG423 |
| D | ARG427 |
| D | HOH637 |
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 | HIS366-PHE377 |
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 | HIS326 | |
| B | HIS326 | |
| C | HIS326 | |
| D | HIS326 |
| 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 | HIS326 | |
| D | HIS326 | |
| D | ASN487 | |
| D | GLN535 | |
| A | ASN487 | |
| A | GLN535 | |
| B | HIS326 | |
| B | ASN487 | |
| B | GLN535 | |
| C | HIS326 | |
| C | ASN487 | |
| C | GLN535 |
| 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 | HIS330 | |
| B | HIS330 | |
| C | HIS330 | |
| D | HIS330 |
| 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 | HIS366 | |
| A | ASP484 | |
| B | HIS366 | |
| B | ASP484 | |
| C | HIS366 | |
| C | ASP484 | |
| D | HIS366 | |
| D | ASP484 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:14609333, ECO:0007744|PDB:1PTW |
| Chain | Residue | Details |
| A | ASP367 | |
| A | PHE538 | |
| B | ASP367 | |
| B | PHE538 | |
| C | ASP367 | |
| C | PHE538 | |
| D | ASP367 | |
| D | PHE538 |
| 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 | LYS251 | |
| B | LYS251 | |
| C | LYS251 | |
| D | LYS251 |
