2WB4
activated diguanylate cyclase PleD in complex with c-di-GMP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000160 | biological_process | phosphorelay signal transduction system |
| A | 0005525 | molecular_function | GTP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0016740 | molecular_function | transferase activity |
| A | 0030154 | biological_process | cell differentiation |
| A | 0043709 | biological_process | cell adhesion involved in single-species biofilm formation |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0052621 | molecular_function | diguanylate cyclase activity |
| A | 1902201 | biological_process | negative regulation of bacterial-type flagellum-dependent cell motility |
| B | 0000160 | biological_process | phosphorelay signal transduction system |
| B | 0005525 | molecular_function | GTP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0016740 | molecular_function | transferase activity |
| B | 0030154 | biological_process | cell differentiation |
| B | 0043709 | biological_process | cell adhesion involved in single-species biofilm formation |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0052621 | molecular_function | diguanylate cyclase activity |
| B | 1902201 | biological_process | negative regulation of bacterial-type flagellum-dependent cell motility |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE BEF A 501 |
| Chain | Residue |
| A | ASP53 |
| A | VAL54 |
| A | MET55 |
| A | THR83 |
| A | ALA84 |
| A | LYS105 |
| A | MG502 |
| A | HOH2002 |
| B | GLU423 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 502 |
| Chain | Residue |
| A | ASP10 |
| A | ASP53 |
| A | MET55 |
| A | BEF501 |
| A | HOH2002 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE C2E A 503 |
| Chain | Residue |
| A | ARG359 |
| A | ASP362 |
| A | ASP383 |
| A | ARG386 |
| A | ILE387 |
| A | ARG390 |
| A | C2E505 |
| A | HOH2020 |
| A | HOH2022 |
| A | HOH2023 |
| B | ARG313 |
| site_id | AC4 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE C2E A 505 |
| Chain | Residue |
| A | SER356 |
| A | ASN357 |
| A | VAL358 |
| A | ARG359 |
| A | ARG390 |
| A | C2E503 |
| A | HOH2024 |
| A | HOH2025 |
| B | SER309 |
| B | LYS312 |
| B | ARG313 |
| B | LEU316 |
| B | GLY317 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1460 |
| Chain | Residue |
| A | ARG117 |
| A | ARG121 |
| B | ARG117 |
| B | ARG121 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE SO4 A 1461 |
| Chain | Residue |
| A | PHE330 |
| A | LYS442 |
| A | ARG446 |
| A | HOH2015 |
| B | ARG168 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE BEF B 501 |
| Chain | Residue |
| B | ASP53 |
| B | VAL54 |
| B | MET55 |
| B | THR83 |
| B | ALA84 |
| B | LYS105 |
| B | MG502 |
| B | HOH2001 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 502 |
| Chain | Residue |
| B | ASP10 |
| B | ASP53 |
| B | MET55 |
| B | BEF501 |
| B | HOH2001 |
| B | HOH2002 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE C2E B 503 |
| Chain | Residue |
| A | ARG313 |
| B | ARG359 |
| B | ASP362 |
| B | ASP383 |
| B | ARG386 |
| B | ILE387 |
| B | ARG390 |
| B | C2E505 |
| site_id | BC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE C2E B 505 |
| Chain | Residue |
| A | SER309 |
| A | ARG313 |
| A | LEU316 |
| A | GLY317 |
| B | SER356 |
| B | ASN357 |
| B | VAL358 |
| B | ARG359 |
| B | ARG390 |
| B | C2E503 |
| B | HOH2018 |
| B | HOH2023 |
| site_id | BC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE C2E B 507 |
| Chain | Residue |
| A | PRO72 |
| A | ARG137 |
| A | GLY144 |
| A | ALA146 |
| A | TYR277 |
| B | PHE331 |
| B | ASN335 |
| B | HIS340 |
| B | ASP344 |
| B | ARG366 |
| B | GLY369 |
| B | GLU370 |
| B | MG509 |
| B | HOH2024 |
| B | HOH2025 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG B 509 |
| Chain | Residue |
| B | C2E507 |
| B | GLY369 |
| B | GLU370 |
| B | GLU371 |
| site_id | BC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 B 1455 |
| Chain | Residue |
| B | ILE328 |
| B | ASP329 |
| B | PHE330 |
| B | PHE331 |
| B | GLU370 |
| B | LYS442 |
| B | ARG446 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255 |
| Chain | Residue | Details |
| A | GLU370 | |
| B | GLU370 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:15569936 |
| Chain | Residue | Details |
| A | ASP9 | |
| B | ASP9 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:15569936, ECO:0000269|PubMed:17697997, ECO:0000269|Ref.6 |
| Chain | Residue | Details |
| A | ASP10 | |
| A | ASP53 | |
| A | MET55 | |
| B | ASP10 | |
| B | ASP53 | |
| B | MET55 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:15569936, ECO:0000305|Ref.6 |
| Chain | Residue | Details |
| A | ASN335 | |
| A | ASP344 | |
| B | ASN335 | |
| B | ASP344 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | SITE: Allosteric product binding, non-activate state |
| Chain | Residue | Details |
| A | ARG178 | |
| B | ARG178 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | SITE: Transition state stabilizer => ECO:0000255 |
| Chain | Residue | Details |
| A | LYS332 | |
| B | LYS332 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | SITE: Allosteric product phosphate group binding, activate and inactive state |
| Chain | Residue | Details |
| A | ARG359 | |
| B | ARG359 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | SITE: Allosteric product binding, activate and inactive state |
| Chain | Residue | Details |
| A | ASP362 | |
| A | ARG390 | |
| B | ASP362 | |
| B | ARG390 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: 4-aspartylphosphate => ECO:0000255|PROSITE-ProRule:PRU00169, ECO:0000269|PubMed:12622822, ECO:0000269|PubMed:15075296 |
| Chain | Residue | Details |
| A | ASP53 | |
| B | ASP53 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17697997 |
| Chain | Residue | Details |
| A | ASP327 | |
| A | ILE328 | |
| A | GLU370 | |
| B | ASP327 | |
| B | ILE328 | |
| B | GLU370 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | SITE: Allosteric product binding, active state |
| Chain | Residue | Details |
| A | ARG313 | |
| B | ARG313 |
