6DVM
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000118 | cellular_component | histone deacetylase complex |
| A | 0004407 | molecular_function | histone deacetylase activity |
| A | 0006325 | biological_process | chromatin organization |
| A | 0016575 | biological_process | histone deacetylation |
| B | 0000118 | cellular_component | histone deacetylase complex |
| B | 0004407 | molecular_function | histone deacetylase activity |
| B | 0006325 | biological_process | chromatin organization |
| B | 0016575 | biological_process | histone deacetylation |
| C | 0000118 | cellular_component | histone deacetylase complex |
| C | 0004407 | molecular_function | histone deacetylase activity |
| C | 0006325 | biological_process | chromatin organization |
| C | 0016575 | biological_process | histone deacetylation |
| D | 0000118 | cellular_component | histone deacetylase complex |
| D | 0004407 | molecular_function | histone deacetylase activity |
| D | 0006325 | biological_process | chromatin organization |
| D | 0016575 | biological_process | histone deacetylation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue ZN A 801 |
| Chain | Residue |
| A | ASP612 |
| A | HIS614 |
| A | ASP705 |
| A | HBJ804 |
| A | HOH901 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue K A 802 |
| Chain | Residue |
| A | LEU634 |
| A | ASP610 |
| A | ASP612 |
| A | HIS614 |
| A | SER633 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue K A 803 |
| Chain | Residue |
| A | PHE623 |
| A | ASP626 |
| A | VAL629 |
| A | TYR662 |
| A | HOH1041 |
| A | HOH1064 |
| site_id | AC4 |
| Number of Residues | 18 |
| Details | binding site for residue HBJ A 804 |
| Chain | Residue |
| A | PRO464 |
| A | SER531 |
| A | HIS574 |
| A | GLY582 |
| A | PHE583 |
| A | ASP612 |
| A | HIS614 |
| A | PHE643 |
| A | ASP705 |
| A | GLY743 |
| A | TYR745 |
| A | ZN801 |
| A | HOH901 |
| A | HOH937 |
| A | HOH965 |
| A | HOH1001 |
| A | HOH1158 |
| A | HOH1184 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 805 |
| Chain | Residue |
| A | MET453 |
| A | LEU454 |
| A | HOH1006 |
| A | HOH1007 |
| A | HOH1038 |
| A | HOH1039 |
| B | MET453 |
| B | LEU454 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue ZN B 801 |
| Chain | Residue |
| B | ASP612 |
| B | HIS614 |
| B | ASP705 |
| B | HBJ804 |
| B | HOH901 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue K B 802 |
| Chain | Residue |
| B | ASP610 |
| B | ASP612 |
| B | HIS614 |
| B | SER633 |
| B | LEU634 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue K B 803 |
| Chain | Residue |
| B | PHE623 |
| B | ASP626 |
| B | VAL629 |
| B | TYR662 |
| B | HOH1071 |
| B | HOH1078 |
| site_id | AC9 |
| Number of Residues | 25 |
| Details | binding site for residue HBJ B 804 |
| Chain | Residue |
| B | ASP460 |
| B | HIS463 |
| B | PRO464 |
| B | SER531 |
| B | HIS573 |
| B | HIS574 |
| B | GLY582 |
| B | PHE583 |
| B | ASP612 |
| B | HIS614 |
| B | PHE643 |
| B | ASP705 |
| B | LEU712 |
| B | GLY743 |
| B | TYR745 |
| B | ZN801 |
| B | HOH901 |
| B | HOH909 |
| B | HOH965 |
| B | HOH1007 |
| B | HOH1151 |
| C | PRO711 |
| C | HBJ804 |
| C | HOH1308 |
| C | HOH1366 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 805 |
| Chain | Residue |
| B | PRO644 |
| B | HOH903 |
| B | HOH904 |
| B | HOH918 |
| B | HOH974 |
| B | HOH1150 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue ZN C 801 |
| Chain | Residue |
| C | ASP612 |
| C | HIS614 |
| C | ASP705 |
| C | HBJ804 |
| C | HOH904 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue K C 802 |
| Chain | Residue |
| C | ASP610 |
| C | ASP612 |
| C | HIS614 |
| C | SER633 |
| C | LEU634 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue K C 803 |
| Chain | Residue |
| C | PHE623 |
| C | ASP626 |
| C | VAL629 |
| C | TYR662 |
| C | HOH1017 |
| C | HOH1073 |
| site_id | AD5 |
| Number of Residues | 20 |
| Details | binding site for residue HBJ C 804 |
| Chain | Residue |
| B | LEU712 |
| B | HBJ804 |
| C | ASP460 |
| C | PRO464 |
| C | SER531 |
| C | HIS574 |
| C | GLY582 |
| C | PHE583 |
| C | ASP612 |
| C | HIS614 |
| C | PHE643 |
| C | ASP705 |
| C | GLY743 |
| C | TYR745 |
| C | ZN801 |
| C | HOH904 |
| C | HOH977 |
| C | HOH1007 |
| C | HOH1043 |
| C | HOH1114 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 805 |
| Chain | Residue |
| A | HOH962 |
| B | MET458 |
| B | ASP460 |
| C | ASN523 |
| C | ASP527 |
| C | HOH908 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 806 |
| Chain | Residue |
| C | LEU557 |
| C | ARG601 |
| C | LEU604 |
| C | GLU696 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 807 |
| Chain | Residue |
| C | ILE510 |
| C | GLU528 |
| C | TYR529 |
| C | HOH920 |
| C | HOH1057 |
| C | HOH1088 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 808 |
| Chain | Residue |
| C | ALA500 |
| C | LEU501 |
| C | CYS502 |
| C | HIS503 |
| C | LYS577 |
| C | HOH999 |
| site_id | AE1 |
| Number of Residues | 1 |
| Details | binding site for residue EDO C 809 |
| Chain | Residue |
| C | ARG788 |
| site_id | AE2 |
| Number of Residues | 9 |
| Details | binding site for residue BTB C 810 |
| Chain | Residue |
| C | GLN450 |
| C | ARG451 |
| C | HOH1050 |
| D | TYR662 |
| D | GLU692 |
| D | PHE793 |
| D | HOH922 |
| D | HOH966 |
| D | HOH1021 |
| site_id | AE3 |
| Number of Residues | 5 |
| Details | binding site for residue ZN D 801 |
| Chain | Residue |
| D | ASP612 |
| D | HIS614 |
| D | ASP705 |
| D | HBJ804 |
| D | HOH906 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue K D 802 |
| Chain | Residue |
| D | ASP610 |
| D | ASP612 |
| D | HIS614 |
| D | SER633 |
| D | LEU634 |
| site_id | AE5 |
| Number of Residues | 6 |
| Details | binding site for residue K D 803 |
| Chain | Residue |
| D | PHE623 |
| D | ASP626 |
| D | VAL629 |
| D | TYR662 |
| D | HOH1003 |
| D | HOH1111 |
| site_id | AE6 |
| Number of Residues | 20 |
| Details | binding site for residue HBJ D 804 |
| Chain | Residue |
| D | ASP460 |
| D | PRO464 |
| D | SER531 |
| D | HIS574 |
| D | GLY582 |
| D | PHE583 |
| D | ASP612 |
| D | HIS614 |
| D | PHE643 |
| D | ASP705 |
| D | GLY743 |
| D | TYR745 |
| D | ZN801 |
| D | EDO805 |
| D | HOH901 |
| D | HOH906 |
| D | HOH982 |
| D | HOH1002 |
| D | HOH1172 |
| D | HOH1199 |
| site_id | AE7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 805 |
| Chain | Residue |
| D | HIS463 |
| D | SER531 |
| D | PHE583 |
| D | HBJ804 |
| D | HOH901 |
| D | HOH908 |
| D | HOH1237 |
| site_id | AE8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 806 |
| Chain | Residue |
| D | ASN457 |
| D | TRP459 |
| D | ASP460 |
| D | HOH907 |
| D | HOH908 |
| site_id | AE9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 807 |
| Chain | Residue |
| D | ASN523 |
| D | ASP527 |
| D | HOH904 |
| D | HOH1022 |
| site_id | AF1 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 808 |
| Chain | Residue |
| D | HIS456 |
| D | ASN457 |
| D | SER461 |
| D | HOH981 |
| D | HOH1042 |
| D | HOH1060 |
| D | HOH1330 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 809 |
| Chain | Residue |
| D | LEU525 |
| D | GLU528 |
| D | TYR529 |
| D | HOH912 |
| D | HOH930 |
| D | HOH968 |
| site_id | AF3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 810 |
| Chain | Residue |
| D | LEU493 |
| D | GLU515 |
| D | TYR539 |
| D | HOH995 |
| D | HOH1108 |
