5B25
Crystal structure of human PDE1B with inhibitor 3
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 601 |
| Chain | Residue |
| A | HIS227 |
| A | HIS263 |
| A | ASP264 |
| A | ASP370 |
| A | HOH733 |
| A | HOH739 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 602 |
| Chain | Residue |
| A | HOH748 |
| A | HOH768 |
| A | HOH865 |
| A | ASP264 |
| A | HOH713 |
| A | HOH733 |
| site_id | AC3 |
| Number of Residues | 19 |
| Details | binding site for residue 4QJ A 603 |
| Chain | Residue |
| A | ILE371 |
| A | HIS373 |
| A | LEU388 |
| A | PHE392 |
| A | LEU409 |
| A | VAL417 |
| A | SER420 |
| A | GLN421 |
| A | GLY423 |
| A | PHE424 |
| A | PHE427 |
| A | GOL607 |
| A | HOH712 |
| A | HOH734 |
| C | GLU441 |
| C | PRO474 |
| C | ASN475 |
| C | VAL478 |
| C | VAL479 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 604 |
| Chain | Residue |
| A | LYS344 |
| A | LYS347 |
| A | HOH811 |
| A | HOH832 |
| A | HOH847 |
| A | HOH848 |
| C | GLN351 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 605 |
| Chain | Residue |
| A | ARG499 |
| A | HOH772 |
| C | PRO221 |
| C | ARG394 |
| C | HOH772 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 606 |
| Chain | Residue |
| A | ARG196 |
| A | LYS198 |
| A | ASN314 |
| A | GLU319 |
| A | HOH737 |
| B | LYS198 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | binding site for residue GOL A 607 |
| Chain | Residue |
| A | THR271 |
| A | GLN395 |
| A | SER407 |
| A | PRO408 |
| A | CYS410 |
| A | 4QJ603 |
| A | HOH706 |
| A | HOH712 |
| A | HOH725 |
| C | PRO476 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue ZN B 601 |
| Chain | Residue |
| B | HIS227 |
| B | HIS263 |
| B | ASP264 |
| B | ASP370 |
| B | HOH702 |
| B | HOH760 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 602 |
| Chain | Residue |
| B | ASP264 |
| B | HOH702 |
| B | HOH714 |
| B | HOH726 |
| B | HOH744 |
| B | HOH862 |
| site_id | AD1 |
| Number of Residues | 21 |
| Details | binding site for residue 4QJ B 603 |
| Chain | Residue |
| A | GLU441 |
| A | PRO474 |
| A | ASN475 |
| A | PRO476 |
| A | VAL478 |
| A | VAL479 |
| B | TYR222 |
| B | ILE371 |
| B | HIS373 |
| B | LEU388 |
| B | PHE392 |
| B | LEU409 |
| B | VAL417 |
| B | SER420 |
| B | GLN421 |
| B | GLY423 |
| B | PHE424 |
| B | PHE427 |
| B | GOL607 |
| B | HOH722 |
| B | HOH723 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 604 |
| Chain | Residue |
| A | GLN351 |
| B | LYS344 |
| B | LYS347 |
| B | HOH785 |
| B | HOH797 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 605 |
| Chain | Residue |
| B | HOH843 |
| D | ARG383 |
| B | TRP378 |
| B | ARG499 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 606 |
| Chain | Residue |
| A | LYS198 |
| B | ARG196 |
| B | ASN314 |
| B | GLU319 |
| site_id | AD5 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 607 |
| Chain | Residue |
| A | LEU447 |
| A | PRO476 |
| B | THR271 |
| B | SER407 |
| B | PRO408 |
| B | CYS410 |
| B | 4QJ603 |
| B | HOH722 |
| site_id | AD6 |
| Number of Residues | 2 |
| Details | binding site for residue GOL B 608 |
| Chain | Residue |
| B | THR278 |
| B | GLU281 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue ZN C 601 |
| Chain | Residue |
| C | HIS227 |
| C | HIS263 |
| C | ASP264 |
| C | ASP370 |
| C | HOH701 |
| C | HOH765 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 602 |
| Chain | Residue |
| C | ASP264 |
| C | HOH701 |
| C | HOH708 |
| C | HOH728 |
| C | HOH781 |
| C | HOH875 |
| site_id | AD9 |
| Number of Residues | 20 |
| Details | binding site for residue 4QJ C 603 |
| Chain | Residue |
| C | TYR222 |
| C | ILE371 |
| C | HIS373 |
| C | LEU388 |
| C | PHE392 |
| C | LEU409 |
| C | VAL417 |
| C | SER420 |
| C | GLN421 |
| C | GLY423 |
| C | PHE424 |
| C | PHE427 |
| C | GOL607 |
| C | HOH711 |
| C | HOH729 |
| D | GLU441 |
| D | PRO474 |
| D | ASN475 |
| D | VAL478 |
| D | VAL479 |
| site_id | AE1 |
| Number of Residues | 10 |
| Details | binding site for residue SO4 C 604 |
| Chain | Residue |
| A | THR316 |
| A | ASP318 |
| C | ARG196 |
| C | SER249 |
| C | GLU250 |
| C | HOH707 |
| C | HOH731 |
| C | HOH778 |
| C | HOH826 |
| C | HOH841 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 605 |
| Chain | Residue |
| C | THR316 |
| C | LYS317 |
| C | HOH817 |
| C | HOH868 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 606 |
| Chain | Residue |
| C | LYS344 |
| C | LYS347 |
| C | HOH871 |
| D | GLN351 |
| site_id | AE4 |
| Number of Residues | 12 |
| Details | binding site for residue GOL C 607 |
| Chain | Residue |
| C | THR271 |
| C | PHE392 |
| C | SER407 |
| C | PRO408 |
| C | CYS410 |
| C | 4QJ603 |
| C | HOH709 |
| C | HOH711 |
| C | HOH712 |
| C | HOH887 |
| D | LEU447 |
| D | PRO476 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 608 |
| Chain | Residue |
| C | THR415 |
| C | VAL417 |
| C | ALA418 |
| C | GLN419 |
| site_id | AE6 |
| Number of Residues | 6 |
| Details | binding site for residue ZN D 601 |
| Chain | Residue |
| D | HIS227 |
| D | HIS263 |
| D | ASP264 |
| D | ASP370 |
| D | HOH703 |
| D | HOH793 |
| site_id | AE7 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 602 |
| Chain | Residue |
| D | ASP264 |
| D | HOH703 |
| D | HOH726 |
| D | HOH732 |
| D | HOH755 |
| D | HOH863 |
| site_id | AE8 |
| Number of Residues | 21 |
| Details | binding site for residue 4QJ D 603 |
| Chain | Residue |
| B | GLU441 |
| B | PRO474 |
| B | ASN475 |
| B | PRO476 |
| B | VAL478 |
| B | VAL479 |
| D | TYR222 |
| D | ILE371 |
| D | HIS373 |
| D | LEU388 |
| D | PHE392 |
| D | LEU409 |
| D | VAL417 |
| D | SER420 |
| D | GLN421 |
| D | GLY423 |
| D | PHE424 |
| D | PHE427 |
| D | GOL607 |
| D | HOH714 |
| D | HOH765 |
| site_id | AE9 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 D 604 |
| Chain | Residue |
| B | THR316 |
| B | ASP318 |
| D | ARG196 |
| D | SER249 |
| D | GLU250 |
| D | HOH713 |
| D | HOH738 |
| D | HOH778 |
| D | HOH831 |
| site_id | AF1 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 605 |
| Chain | Residue |
| D | THR316 |
| D | LYS317 |
| D | HOH832 |
| D | HOH860 |
| site_id | AF2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 D 606 |
| Chain | Residue |
| B | GLN351 |
| D | LYS344 |
| D | LYS347 |
| D | HOH781 |
| D | HOH861 |
| site_id | AF3 |
| Number of Residues | 10 |
| Details | binding site for residue GOL D 607 |
| Chain | Residue |
| B | PRO476 |
| D | THR271 |
| D | SER407 |
| D | PRO408 |
| D | CYS410 |
| D | 4QJ603 |
| D | HOH701 |
| D | HOH737 |
| D | HOH740 |
| D | HOH765 |
Functional Information from PROSITE/UniProt
| site_id | PS00126 |
| Number of Residues | 12 |
| Details | PDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDYeHtGttNsF |
| Chain | Residue | Details |
| A | HIS263-PHE274 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton donor => ECO:0000250|UniProtKB:O76083 |
| Chain | Residue | Details |
| A | HIS223 | |
| B | HIS223 | |
| C | HIS223 | |
| D | HIS223 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:15260978, ECO:0007744|PDB:1TAZ, ECO:0007744|PDB:4NPV, ECO:0007744|PDB:4NPW |
| Chain | Residue | Details |
| C | HIS227 | |
| C | HIS263 | |
| C | ASP264 | |
| C | ASP370 | |
| D | HIS227 | |
| D | HIS263 | |
| D | ASP264 | |
| D | ASP370 | |
| A | ASP264 | |
| A | ASP370 | |
| A | HIS227 | |
| A | HIS263 | |
| B | HIS227 | |
| B | HIS263 | |
| B | ASP264 | |
| B | ASP370 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q01065 |
| Chain | Residue | Details |
| A | ILE489 | |
| B | ILE489 | |
| C | ILE489 | |
| D | ILE489 |
