5VI6
Crystal structure of histone deacetylase 8 in complex with trapoxin A
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000118 | cellular_component | histone deacetylase complex |
| A | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| A | 0000228 | cellular_component | nuclear chromosome |
| A | 0004407 | molecular_function | histone deacetylase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006351 | biological_process | DNA-templated transcription |
| A | 0007064 | biological_process | mitotic sister chromatid cohesion |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0030544 | molecular_function | Hsp70 protein binding |
| A | 0031397 | biological_process | negative regulation of protein ubiquitination |
| A | 0031507 | biological_process | heterochromatin formation |
| A | 0031647 | biological_process | regulation of protein stability |
| A | 0032204 | biological_process | regulation of telomere maintenance |
| A | 0033558 | molecular_function | protein lysine deacetylase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051879 | molecular_function | Hsp90 protein binding |
| A | 0140297 | molecular_function | DNA-binding transcription factor binding |
| A | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| A | 0160008 | molecular_function | protein decrotonylase activity |
| A | 0160009 | molecular_function | histone decrotonylase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | ASP178 |
| A | HIS180 |
| A | ASP267 |
| B | 5OM4 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue K A 402 |
| Chain | Residue |
| A | ASP176 |
| A | ASP178 |
| A | HIS180 |
| A | SER199 |
| A | LEU200 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue K A 403 |
| Chain | Residue |
| A | PHE189 |
| A | THR192 |
| A | VAL195 |
| A | TYR225 |
| A | HOH590 |
| A | HOH730 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | SER63 |
| A | MET64 |
| A | ASP355 |
| A | HOH616 |
| A | HOH686 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | ARG166 |
| A | ARG167 |
| A | GLU170 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | GLU23 |
| A | TYR24 |
| A | ALA114 |
| A | HOH601 |
| A | HOH631 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | MET274 |
| site_id | AC8 |
| Number of Residues | 9 |
| Details | binding site for residue EDO A 408 |
| Chain | Residue |
| A | PRO281 |
| A | VAL282 |
| A | ARG313 |
| A | TYR317 |
| A | LEU346 |
| A | GLU347 |
| A | ILE348 |
| A | HOH531 |
| A | HOH604 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 409 |
| Chain | Residue |
| A | GLY206 |
| A | PHE207 |
| A | PHE208 |
| A | PRO209 |
| A | GLY210 |
| site_id | AD1 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 410 |
| Chain | Residue |
| A | HIS143 |
| A | LYS145 |
| A | SER150 |
| A | ASP183 |
| A | PHE208 |
| A | PRO209 |
| A | HOH548 |
| A | HOH632 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 411 |
| Chain | Residue |
| A | TYR111 |
| A | TRP141 |
| A | PHE152 |
| A | CYS153 |
| A | TYR154 |
| A | LEU155 |
| site_id | AD3 |
| Number of Residues | 9 |
| Details | binding site for residue EDO A 412 |
| Chain | Residue |
| A | CYS28 |
| A | ILE34 |
| A | ARG37 |
| A | ALA38 |
| A | SER138 |
| A | HOH502 |
| A | HOH505 |
| A | HOH519 |
| A | HOH657 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 413 |
| Chain | Residue |
| A | ARG361 |
| A | GLN364 |
| A | TYR368 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue DIO A 414 |
| Chain | Residue |
| A | TYR224 |
| A | TYR225 |
| A | ALA254 |
| A | ASN372 |
| A | LEU373 |
| A | HOH681 |
| site_id | AD6 |
| Number of Residues | 4 |
| Details | binding site for residue DIO A 415 |
| Chain | Residue |
| A | THR69 |
| A | LEU163 |
| A | ALA188 |
| A | PHE189 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"19053282","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 3 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19053282","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"17721440","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"15242608","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
