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 |
A | HIS227 | |
C | HIS263 | |
C | ASP264 | |
C | ASP370 | |
D | HIS227 | |
D | HIS263 | |
D | ASP264 | |
D | ASP370 | |
A | HIS263 | |
A | ASP264 | |
A | ASP370 | |
B | HIS227 | |
B | HIS263 | |
B | ASP264 | |
B | ASP370 | |
C | HIS227 |
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 |