6HU0
Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 9
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004407 | molecular_function | histone deacetylase activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0006325 | biological_process | chromatin organization |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0031507 | biological_process | heterochromatin formation |
| A | 0040029 | biological_process | epigenetic regulation of gene expression |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| B | 0004407 | molecular_function | histone deacetylase activity |
| B | 0005634 | cellular_component | nucleus |
| B | 0006325 | biological_process | chromatin organization |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0031507 | biological_process | heterochromatin formation |
| B | 0040029 | biological_process | epigenetic regulation of gene expression |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| C | 0004407 | molecular_function | histone deacetylase activity |
| C | 0005634 | cellular_component | nucleus |
| C | 0006325 | biological_process | chromatin organization |
| C | 0016787 | molecular_function | hydrolase activity |
| C | 0031507 | biological_process | heterochromatin formation |
| C | 0040029 | biological_process | epigenetic regulation of gene expression |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| D | 0004407 | molecular_function | histone deacetylase activity |
| D | 0005634 | cellular_component | nucleus |
| D | 0006325 | biological_process | chromatin organization |
| D | 0016787 | molecular_function | hydrolase activity |
| D | 0031507 | biological_process | heterochromatin formation |
| D | 0040029 | biological_process | epigenetic regulation of gene expression |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 501 |
| Chain | Residue |
| A | ASP186 |
| A | HIS188 |
| A | ASP285 |
| A | T86504 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue K A 502 |
| Chain | Residue |
| A | ASP184 |
| A | ASP186 |
| A | HIS188 |
| A | SER207 |
| A | VAL208 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue K A 503 |
| Chain | Residue |
| A | PHE197 |
| A | SER200 |
| A | VAL203 |
| A | SER243 |
| A | HOH799 |
| site_id | AC4 |
| Number of Residues | 18 |
| Details | binding site for residue T86 A 504 |
| Chain | Residue |
| A | LYS20 |
| A | ASP100 |
| A | HIS141 |
| A | HIS142 |
| A | GLY150 |
| A | ASP186 |
| A | HIS188 |
| A | PHE216 |
| A | ASP285 |
| A | PRO291 |
| A | HIS292 |
| A | TYR341 |
| A | ZN501 |
| A | HOH831 |
| A | HOH916 |
| B | ASP50 |
| B | HOH616 |
| B | HOH859 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue DMF A 505 |
| Chain | Residue |
| A | ASP9 |
| A | ARG43 |
| A | HOH623 |
| B | GLU147 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue DMF A 506 |
| Chain | Residue |
| A | TYR7 |
| A | MET29 |
| A | ASP30 |
| A | ASN33 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue DMF A 507 |
| Chain | Residue |
| A | TYR301 |
| A | ARG352 |
| A | ALA355 |
| A | LEU356 |
| A | GLU359 |
| site_id | AC8 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 508 |
| Chain | Residue |
| A | HIS189 |
| A | GLU194 |
| A | THR219 |
| A | GLY220 |
| A | THR221 |
| A | ASN223 |
| A | PHE233 |
| A | LEU234 |
| A | HOH764 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 509 |
| Chain | Residue |
| A | ARG12 |
| A | GLN13 |
| A | HOH609 |
| A | HOH631 |
| A | HOH761 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue GOL A 510 |
| Chain | Residue |
| A | ASP93 |
| A | SER94 |
| A | SER96 |
| B | TYR7 |
| B | ARG43 |
| B | HOH696 |
| B | HOH809 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 511 |
| Chain | Residue |
| A | GLU131 |
| A | VAL132 |
| A | LEU327 |
| A | LYS330 |
| A | VAL331 |
| A | HOH625 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 512 |
| Chain | Residue |
| A | GLN10 |
| A | TYR11 |
| A | LEU14 |
| A | GLN48 |
| A | GLN116 |
| A | HOH601 |
| site_id | AD4 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 513 |
| Chain | Residue |
| A | GLN75 |
| A | CYS79 |
| A | PRO105 |
| A | ASP109 |
| A | HOH611 |
| B | TRP222 |
| B | ASN223 |
| B | MET224 |
| B | PRO231 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 514 |
| Chain | Residue |
| A | PRO45 |
| A | LEU47 |
| A | ALA120 |
| A | HOH821 |
| B | TYR99 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 515 |
| Chain | Residue |
| A | ALA211 |
| A | TRP222 |
| A | PRO248 |
| A | GLU250 |
| A | HIS407 |
| A | HOH617 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue ZN B 501 |
| Chain | Residue |
| B | HIS188 |
| B | ASP285 |
| B | T86504 |
| B | ASP186 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue K B 502 |
| Chain | Residue |
| B | ASP184 |
| B | ASP186 |
| B | HIS188 |
| B | SER207 |
| B | VAL208 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue K B 503 |
| Chain | Residue |
| B | PHE197 |
| B | SER200 |
| B | VAL203 |
| B | SER243 |
| B | HOH815 |
| site_id | AE1 |
| Number of Residues | 16 |
| Details | binding site for residue T86 B 504 |
| Chain | Residue |
| A | ASP50 |
| A | HOH607 |
| A | HOH796 |
| B | LYS20 |
| B | ASP100 |
| B | HIS141 |
| B | HIS142 |
| B | GLY150 |
| B | ASP186 |
| B | HIS188 |
| B | PHE216 |
| B | ASP285 |
| B | HIS292 |
| B | TYR341 |
| B | ZN501 |
| B | HOH814 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue DMF B 505 |
| Chain | Residue |
| B | TYR7 |
| B | MET29 |
| B | ASP30 |
| B | ILE38 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue DMF B 506 |
| Chain | Residue |
| B | ILE253 |
| B | ASP257 |
| B | ASP402 |
| B | ILE404 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue DMF B 507 |
| Chain | Residue |
| B | GLU131 |
| B | VAL132 |
| B | LYS330 |
| B | VAL331 |
| B | VAL361 |
| B | HOH702 |
| site_id | AE5 |
| Number of Residues | 7 |
| Details | binding site for residue DMF B 508 |
| Chain | Residue |
| B | ALA211 |
| B | THR221 |
| B | TRP222 |
| B | PRO248 |
| B | LEU249 |
| B | GLU250 |
| B | HIS407 |
| site_id | AE6 |
| Number of Residues | 3 |
| Details | binding site for residue DMF B 510 |
| Chain | Residue |
| B | PRO19 |
| B | LYS20 |
| B | HOH687 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue DMF B 511 |
| Chain | Residue |
| B | ARG12 |
| B | GLN13 |
| B | TYR377 |
| site_id | AE8 |
| Number of Residues | 4 |
| Details | binding site for residue DMF B 512 |
| Chain | Residue |
| B | LYS325 |
| B | SER328 |
| B | HOH679 |
| B | HOH713 |
| site_id | AE9 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 513 |
| Chain | Residue |
| B | HIS189 |
| B | GLU194 |
| B | THR219 |
| B | GLY220 |
| B | THR221 |
| B | PHE233 |
| B | LEU234 |
| B | ASN246 |
| site_id | AF1 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 514 |
| Chain | Residue |
| A | HOH815 |
| B | GLN10 |
| B | TYR11 |
| B | LEU14 |
| B | GLN48 |
| B | GLN116 |
| B | HOH612 |
| site_id | AF2 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 515 |
| Chain | Residue |
| B | TYR35 |
| B | LYS36 |
| B | LYS365 |
| B | MET366 |
| B | THR367 |
| B | HOH610 |
| B | HOH672 |
| D | THR85 |
| site_id | AF3 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 516 |
| Chain | Residue |
| A | TYR99 |
| B | VAL44 |
| B | PRO45 |
| B | ALA120 |
| B | SER123 |
| B | ALA124 |
| B | HOH820 |
| site_id | AF4 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 517 |
| Chain | Residue |
| B | TYR301 |
| B | ARG352 |
| B | ALA355 |
| B | LEU356 |
| B | GLU359 |
| B | MET366 |
| B | ILE368 |
| site_id | AF5 |
| Number of Residues | 4 |
| Details | binding site for residue ZN C 501 |
| Chain | Residue |
| C | ASP186 |
| C | HIS188 |
| C | ASP285 |
| C | T86504 |
| site_id | AF6 |
| Number of Residues | 5 |
| Details | binding site for residue K C 502 |
| Chain | Residue |
| C | ASP184 |
| C | ASP186 |
| C | HIS188 |
| C | SER207 |
| C | VAL208 |
| site_id | AF7 |
| Number of Residues | 5 |
| Details | binding site for residue K C 503 |
| Chain | Residue |
| C | PHE197 |
| C | SER200 |
| C | VAL203 |
| C | SER243 |
| C | HOH824 |
| site_id | AF8 |
| Number of Residues | 16 |
| Details | binding site for residue T86 C 504 |
| Chain | Residue |
| C | LYS20 |
| C | ASP100 |
| C | HIS141 |
| C | HIS142 |
| C | GLY150 |
| C | ASP186 |
| C | HIS188 |
| C | PHE216 |
| C | ASP285 |
| C | PRO291 |
| C | HIS292 |
| C | TYR341 |
| C | ZN501 |
| C | HOH698 |
| D | ASP50 |
| D | HOH854 |
| site_id | AF9 |
| Number of Residues | 6 |
| Details | binding site for residue DMF C 505 |
| Chain | Residue |
| C | TYR7 |
| C | MET29 |
| C | ASP30 |
| C | ASN33 |
| C | DMF507 |
| C | HOH700 |
| site_id | AG1 |
| Number of Residues | 6 |
| Details | binding site for residue DMF C 506 |
| Chain | Residue |
| C | LEU90 |
| C | ASP93 |
| C | SER94 |
| D | ILE38 |
| D | LEU41 |
| D | ARG43 |
| site_id | AG2 |
| Number of Residues | 7 |
| Details | binding site for residue DMF C 507 |
| Chain | Residue |
| C | ILE5 |
| C | TYR7 |
| C | ILE38 |
| C | ARG43 |
| C | DMF505 |
| C | HOH732 |
| D | DMF508 |
| site_id | AG3 |
| Number of Residues | 6 |
| Details | binding site for residue DMF C 509 |
| Chain | Residue |
| C | TYR301 |
| C | ARG352 |
| C | LEU356 |
| C | GLU359 |
| C | MET366 |
| C | ILE368 |
| site_id | AG4 |
| Number of Residues | 5 |
| Details | binding site for residue DMF C 510 |
| Chain | Residue |
| B | GLU360 |
| B | VAL361 |
| B | LYS362 |
| B | HOH690 |
| C | GLY363 |
| site_id | AG5 |
| Number of Residues | 5 |
| Details | binding site for residue DMF C 511 |
| Chain | Residue |
| C | LYS324 |
| C | LYS325 |
| C | SER328 |
| C | HOH625 |
| C | HOH760 |
| site_id | AG6 |
| Number of Residues | 3 |
| Details | binding site for residue DMF C 512 |
| Chain | Residue |
| C | SER376 |
| C | TYR377 |
| C | GOL517 |
| site_id | AG7 |
| Number of Residues | 5 |
| Details | binding site for residue DMF C 513 |
| Chain | Residue |
| B | PRO383 |
| C | ARG409 |
| C | SER442 |
| C | LEU443 |
| C | GOL522 |
| site_id | AG8 |
| Number of Residues | 6 |
| Details | binding site for residue DMF C 514 |
| Chain | Residue |
| A | GLU40 |
| A | LYS365 |
| A | MET366 |
| A | THR367 |
| C | THR65 |
| C | HOH889 |
| site_id | AG9 |
| Number of Residues | 7 |
| Details | binding site for residue DMF C 515 |
| Chain | Residue |
| C | GLN10 |
| C | TYR11 |
| C | PRO46 |
| C | GLN48 |
| C | GLN116 |
| C | HOH800 |
| D | PRO217 |
| site_id | AH1 |
| Number of Residues | 5 |
| Details | binding site for residue DMF C 516 |
| Chain | Residue |
| C | TRP198 |
| C | GLY236 |
| C | ALA237 |
| C | HOH628 |
| C | HOH656 |
| site_id | AH2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL C 517 |
| Chain | Residue |
| C | ARG12 |
| C | CYS16 |
| C | TYR377 |
| C | DMF512 |
| C | HOH799 |
| C | HOH920 |
| site_id | AH3 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 518 |
| Chain | Residue |
| C | GLU131 |
| C | LEU327 |
| C | LYS330 |
| C | VAL331 |
| C | PRO332 |
| C | HOH635 |
| C | HOH639 |
| site_id | AH4 |
| Number of Residues | 9 |
| Details | binding site for residue GOL C 519 |
| Chain | Residue |
| C | HIS189 |
| C | GLU194 |
| C | THR219 |
| C | GLY220 |
| C | THR221 |
| C | PHE233 |
| C | LEU234 |
| C | ASN246 |
| C | HOH739 |
| site_id | AH5 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 520 |
| Chain | Residue |
| C | ILE253 |
| C | ASP257 |
| C | ASP402 |
| C | ILE404 |
| C | HOH627 |
| C | HOH637 |
| C | HOH723 |
| site_id | AH6 |
| Number of Residues | 9 |
| Details | binding site for residue GOL C 521 |
| Chain | Residue |
| A | THR85 |
| C | TYR35 |
| C | LYS36 |
| C | LYS365 |
| C | MET366 |
| C | THR367 |
| C | HOH618 |
| C | HOH667 |
| C | HOH714 |
| site_id | AH7 |
| Number of Residues | 5 |
| Details | binding site for residue GOL C 522 |
| Chain | Residue |
| C | ARG409 |
| C | ARG410 |
| C | DMF513 |
| C | HOH617 |
| C | HOH680 |
| site_id | AH8 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 523 |
| Chain | Residue |
| A | GLU371 |
| A | HOH622 |
| A | HOH736 |
| C | GLU195 |
| C | TRP198 |
| C | HOH604 |
| C | HOH707 |
| site_id | AH9 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 524 |
| Chain | Residue |
| C | ASP267 |
| C | ASN270 |
| C | ILE271 |
| C | TRP329 |
| C | HOH646 |
| C | HOH783 |
| C | HOH848 |
| site_id | AI1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN D 501 |
| Chain | Residue |
| D | ASP186 |
| D | HIS188 |
| D | ASP285 |
| D | T86504 |
| site_id | AI2 |
| Number of Residues | 5 |
| Details | binding site for residue K D 502 |
| Chain | Residue |
| D | ASP184 |
| D | ASP186 |
| D | HIS188 |
| D | SER207 |
| D | VAL208 |
| site_id | AI3 |
| Number of Residues | 5 |
| Details | binding site for residue K D 503 |
| Chain | Residue |
| D | PHE197 |
| D | SER200 |
| D | VAL203 |
| D | SER243 |
| D | HOH819 |
| site_id | AI4 |
| Number of Residues | 16 |
| Details | binding site for residue T86 D 504 |
| Chain | Residue |
| C | ASP50 |
| C | HOH605 |
| D | LYS20 |
| D | ASP100 |
| D | HIS141 |
| D | HIS142 |
| D | ASP186 |
| D | HIS188 |
| D | PHE216 |
| D | ASP285 |
| D | PRO291 |
| D | HIS292 |
| D | TYR341 |
| D | ZN501 |
| D | HOH742 |
| D | HOH788 |
| site_id | AI5 |
| Number of Residues | 6 |
| Details | binding site for residue DMF D 505 |
| Chain | Residue |
| D | TYR35 |
| D | LYS36 |
| D | LEU37 |
| D | MET366 |
| D | THR367 |
| D | HOH700 |
| site_id | AI6 |
| Number of Residues | 6 |
| Details | binding site for residue DMF D 506 |
| Chain | Residue |
| D | TYR301 |
| D | ARG352 |
| D | GLU359 |
| D | MET366 |
| D | HOH606 |
| D | HOH677 |
| site_id | AI7 |
| Number of Residues | 4 |
| Details | binding site for residue DMF D 507 |
| Chain | Residue |
| D | GLU131 |
| D | VAL132 |
| D | LYS330 |
| D | VAL331 |
| site_id | AI8 |
| Number of Residues | 5 |
| Details | binding site for residue DMF D 508 |
| Chain | Residue |
| C | ARG43 |
| C | DMF507 |
| D | ASP93 |
| D | SER94 |
| D | SER96 |
| site_id | AI9 |
| Number of Residues | 7 |
| Details | binding site for residue DMF D 509 |
| Chain | Residue |
| D | TYR7 |
| D | ARG12 |
| D | MET29 |
| D | ASP30 |
| D | ASN33 |
| D | ILE38 |
| D | HOH870 |
| site_id | AJ1 |
| Number of Residues | 8 |
| Details | binding site for residue GOL D 510 |
| Chain | Residue |
| C | GLY214 |
| C | HOH766 |
| D | GLN10 |
| D | TYR11 |
| D | LEU14 |
| D | GLN48 |
| D | GLN116 |
| D | HOH617 |
| site_id | AJ2 |
| Number of Residues | 8 |
| Details | binding site for residue GOL D 511 |
| Chain | Residue |
| D | HIS189 |
| D | GLU194 |
| D | GLY220 |
| D | THR221 |
| D | PHE233 |
| D | LEU234 |
| D | ASN246 |
| D | HOH710 |
| site_id | AJ3 |
| Number of Residues | 4 |
| Details | binding site for residue GOL D 512 |
| Chain | Residue |
| D | LEU256 |
| D | ASN260 |
| D | TYR321 |
| D | HOH660 |
| site_id | AJ4 |
| Number of Residues | 3 |
| Details | binding site for residue GOL D 513 |
| Chain | Residue |
| D | GLU359 |
| D | GLU360 |
| D | HOH845 |
| site_id | AJ5 |
| Number of Residues | 12 |
| Details | binding site for residues DMF B 509 and GOL C 525 |
| Chain | Residue |
| B | ARG409 |
| B | SER442 |
| B | LEU443 |
| B | HOH943 |
| C | TYR301 |
| C | ARG352 |
| C | LEU356 |
| C | GLU359 |
| C | MET366 |
| C | ILE368 |
| C | PRO383 |
| C | PRO383 |
| site_id | AJ6 |
| Number of Residues | 8 |
| Details | binding site for residues DMF C 508 and GOL C 526 |
| Chain | Residue |
| A | ASN303 |
| A | ILE368 |
| C | ALA61 |
| C | PHE62 |
| C | ARG145 |
| C | HIS162 |
| C | ALA196 |
| C | HOH871 |
