2VMF
Structural and biochemical evidence for a boat-like transition state in beta-mannosidases
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| A | 0004567 | molecular_function | beta-mannosidase activity |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005764 | cellular_component | lysosome |
| A | 0005975 | biological_process | carbohydrate metabolic process |
| A | 0006516 | biological_process | glycoprotein catabolic process |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
| B | 0004553 | molecular_function | hydrolase activity, hydrolyzing O-glycosyl compounds |
| B | 0004567 | molecular_function | beta-mannosidase activity |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005764 | cellular_component | lysosome |
| B | 0005975 | biological_process | carbohydrate metabolic process |
| B | 0006516 | biological_process | glycoprotein catabolic process |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE MVL A1865 |
| Chain | Residue |
| A | TRP198 |
| A | TRP645 |
| A | TRP656 |
| A | EDO1876 |
| A | ASP199 |
| A | TRP200 |
| A | TRP395 |
| A | ASN461 |
| A | GLU462 |
| A | TRP533 |
| A | TYR537 |
| A | GLU555 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A1866 |
| Chain | Residue |
| A | GLN365 |
| A | ASN648 |
| A | ASP649 |
| A | ILE659 |
| A | ASP660 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO A1867 |
| Chain | Residue |
| A | TRP519 |
| A | TRP525 |
| A | SER530 |
| A | ASN532 |
| A | ASP548 |
| A | PRO550 |
| A | MET553 |
| A | HOH2461 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A1868 |
| Chain | Residue |
| A | ILE328 |
| A | GLY329 |
| A | ASN450 |
| A | HIS451 |
| A | ALA452 |
| A | ARG507 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A1869 |
| Chain | Residue |
| A | GLN230 |
| A | ARG331 |
| A | ASP506 |
| A | ARG507 |
| A | HOH2462 |
| A | HOH2463 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A1870 |
| Chain | Residue |
| A | GLU465 |
| A | LYS468 |
| A | TYR469 |
| A | PRO514 |
| A | LEU516 |
| A | ALA517 |
| A | ASN518 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A1871 |
| Chain | Residue |
| A | ARG597 |
| A | PRO607 |
| A | GLU608 |
| A | SER609 |
| A | PHE610 |
| A | PHE613 |
| A | HOH2336 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A1872 |
| Chain | Residue |
| A | ASN337 |
| A | HIS511 |
| A | TYR515 |
| A | HOH2464 |
| A | HOH2465 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A1873 |
| Chain | Residue |
| A | ARG634 |
| A | GLN686 |
| A | TYR693 |
| A | HOH2321 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A1874 |
| Chain | Residue |
| A | SER825 |
| A | THR842 |
| A | HOH2466 |
| site_id | BC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A1875 |
| Chain | Residue |
| A | SER43 |
| A | GLN44 |
| A | SER45 |
| A | GLY46 |
| A | THR47 |
| A | GLU48 |
| A | GLU90 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO A1876 |
| Chain | Residue |
| A | ASN178 |
| A | ASP199 |
| A | CYS424 |
| A | GLU462 |
| A | TRP470 |
| A | MVL1865 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A1877 |
| Chain | Residue |
| A | PHE775 |
| A | PHE776 |
| site_id | BC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO A1878 |
| Chain | Residue |
| A | HIS326 |
| A | ARG327 |
| A | ASP407 |
| A | ASN450 |
| A | HIS451 |
| A | HOH2249 |
| A | HOH2275 |
| A | HOH2467 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A1879 |
| Chain | Residue |
| A | PHE42 |
| A | SER43 |
| A | GLN44 |
| A | THR47 |
| A | LYS49 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A1880 |
| Chain | Residue |
| A | ASP88 |
| A | HIS157 |
| A | ARG161 |
| B | ARG161 |
| site_id | BC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR A1882 |
| Chain | Residue |
| A | HIS284 |
| site_id | BC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE BR A1881 |
| Chain | Residue |
| A | ILE107 |
| A | LYS142 |
| site_id | CC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR A1882 |
| Chain | Residue |
| A | HIS284 |
| site_id | CC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR A1884 |
| Chain | Residue |
| A | GLN108 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE BR A1885 |
| Chain | Residue |
| A | GLN685 |
| A | ASP688 |
| site_id | CC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR A1886 |
| Chain | Residue |
| A | THR477 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL A1887 |
| Chain | Residue |
| A | ILE684 |
| A | GLN685 |
| A | HOH2392 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A1888 |
| Chain | Residue |
| A | TYR347 |
| A | PRO637 |
| A | MET640 |
| A | HOH2370 |
| A | HOH2468 |
| site_id | CC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE BR A1889 |
| Chain | Residue |
| A | GLN577 |
| A | ILE578 |
| A | GLU579 |
| site_id | CC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR A1890 |
| Chain | Residue |
| A | ASN402 |
| site_id | CC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL A1891 |
| Chain | Residue |
| A | ARG447 |
| A | HOH2269 |
| site_id | DC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO A1892 |
| Chain | Residue |
| A | GLU708 |
| A | MET709 |
| A | LYS710 |
| A | LYS758 |
| A | ILE760 |
| site_id | DC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A1893 |
| Chain | Residue |
| A | ASP105 |
| A | VAL250 |
| A | GLN252 |
| site_id | DC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR A1894 |
| Chain | Residue |
| A | ARG626 |
| site_id | DC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO A1895 |
| Chain | Residue |
| A | ASP119 |
| A | LYS129 |
| A | HIS157 |
| A | GLN162 |
| B | ASP119 |
| B | LYS129 |
| B | HIS157 |
| B | GLN162 |
| site_id | DC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A1896 |
| Chain | Residue |
| A | ARG296 |
| A | MET298 |
| A | THR304 |
| A | THR306 |
| site_id | DC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL A1897 |
| Chain | Residue |
| A | ASN77 |
| A | HOH2018 |
| A | HOH2032 |
| site_id | DC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE MVL B1868 |
| Chain | Residue |
| B | TRP198 |
| B | ASP199 |
| B | TRP200 |
| B | TRP395 |
| B | ASN461 |
| B | GLU462 |
| B | TRP533 |
| B | TYR537 |
| B | GLU555 |
| B | TRP645 |
| B | TRP656 |
| B | EDO1874 |
| site_id | DC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B1869 |
| Chain | Residue |
| B | TRP519 |
| B | TRP525 |
| B | SER530 |
| B | ASN532 |
| B | ASP548 |
| B | PRO550 |
| site_id | DC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B1870 |
| Chain | Residue |
| B | ARG331 |
| B | ASP506 |
| B | ARG507 |
| B | EDO1899 |
| B | HOH2218 |
| B | HOH2472 |
| site_id | EC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B1871 |
| Chain | Residue |
| B | SER43 |
| B | GLN44 |
| B | GLY46 |
| B | THR47 |
| B | GLU48 |
| B | GLU90 |
| site_id | EC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B1872 |
| Chain | Residue |
| B | GLN365 |
| B | ASN648 |
| B | ASP649 |
| B | ILE659 |
| B | ASP660 |
| site_id | EC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B1873 |
| Chain | Residue |
| B | GLU465 |
| B | LYS468 |
| B | TYR469 |
| B | PRO514 |
| B | LEU516 |
| B | ALA517 |
| B | ASN518 |
| site_id | EC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B1874 |
| Chain | Residue |
| B | ASN178 |
| B | ASP199 |
| B | CYS424 |
| B | GLU462 |
| B | TRP470 |
| B | MVL1868 |
| site_id | EC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B1875 |
| Chain | Residue |
| B | PHE356 |
| B | ARG633 |
| B | ARG636 |
| B | ILE695 |
| B | SER696 |
| B | ASP697 |
| B | ASN733 |
| B | THR734 |
| site_id | EC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B1876 |
| Chain | Residue |
| B | ILE328 |
| B | GLY329 |
| B | ARG449 |
| B | ASN450 |
| B | HIS451 |
| B | ALA452 |
| B | ARG507 |
| site_id | EC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B1877 |
| Chain | Residue |
| B | PHE775 |
| B | ARG777 |
| B | LYS778 |
| B | HOH2473 |
| site_id | EC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B1878 |
| Chain | Residue |
| B | PHE42 |
| B | SER43 |
| B | GLN44 |
| B | THR47 |
| B | LYS49 |
| site_id | EC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE BR B1879 |
| Chain | Residue |
| B | ILE107 |
| B | LYS142 |
| B | HOH2084 |
| site_id | FC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE BR B1880 |
| Chain | Residue |
| B | GLN685 |
| B | ASP688 |
| site_id | FC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR B1881 |
| Chain | Residue |
| B | HOH2320 |
| site_id | FC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE BR B1882 |
| Chain | Residue |
| B | THR477 |
| site_id | FC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL B1883 |
| Chain | Residue |
| B | TYR443 |
| B | ARG446 |
| site_id | FC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL B1884 |
| Chain | Residue |
| B | HIS181 |
| B | HOH2116 |
| site_id | FC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CL B1885 |
| Chain | Residue |
| B | GLN108 |
| site_id | FC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL B1886 |
| Chain | Residue |
| B | GLN685 |
| B | HOH2404 |
| site_id | FC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B1888 |
| Chain | Residue |
| B | ARG376 |
| B | TYR661 |
| site_id | FC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B1889 |
| Chain | Residue |
| B | HIS326 |
| B | ARG327 |
| B | ASP407 |
| B | ASN450 |
| B | HIS451 |
| B | HOH2212 |
| B | HOH2288 |
| B | HOH2474 |
| site_id | GC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B1890 |
| Chain | Residue |
| B | PRO637 |
| B | HOH2385 |
| B | HOH2475 |
| site_id | GC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE BR B1891 |
| Chain | Residue |
| B | ASN300 |
| B | ASN390 |
| B | HOH2234 |
| site_id | GC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B1892 |
| Chain | Residue |
| B | MET298 |
| B | TRP302 |
| B | ASN351 |
| site_id | GC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B1893 |
| Chain | Residue |
| B | GLN324 |
| B | SER325 |
| B | HOH2209 |
| site_id | GC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B1894 |
| Chain | Residue |
| B | ASN261 |
| B | HOH2477 |
| site_id | GC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE BR B1901 |
| Chain | Residue |
| B | ARG626 |
| B | HOH2473 |
| site_id | GC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B1895 |
| Chain | Residue |
| B | LEU307 |
| B | ASP309 |
| B | ARG327 |
| B | HOH2167 |
| site_id | GC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B1896 |
| Chain | Residue |
| B | LYS565 |
| B | THR817 |
| B | PRO818 |
| B | HOH2354 |
| B | HOH2478 |
| site_id | GC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL B1897 |
| Chain | Residue |
| B | GLN577 |
| B | ILE578 |
| site_id | HC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B1898 |
| Chain | Residue |
| B | ILE282 |
| B | HIS284 |
| B | HOH2479 |
| site_id | HC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO B1899 |
| Chain | Residue |
| B | GLN230 |
| B | LEU231 |
| B | THR332 |
| B | ASP506 |
| B | EDO1870 |
| B | HOH2480 |
| site_id | HC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO B1900 |
| Chain | Residue |
| B | TRP665 |
| B | TYR670 |
| B | ARG823 |
| B | TYR824 |
| B | HOH2481 |
| site_id | HC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A1899 |
| Chain | Residue |
| A | ASN300 |
| A | TRP302 |
| A | PHE356 |
| A | LYS358 |
| A | ASN390 |
| A | ASP697 |
| A | HOH2217 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1bgl |
| Chain | Residue | Details |
| A | GLU462 | |
| A | GLU555 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1bgl |
| Chain | Residue | Details |
| B | GLU462 | |
| B | GLU555 |
