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 | 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 | 0031647 | biological_process | regulation of protein stability |
A | 0032204 | biological_process | regulation of telomere maintenance |
A | 0033558 | molecular_function | protein lysine deacetylase activity |
A | 0040029 | biological_process | epigenetic regulation of gene expression |
A | 0046872 | molecular_function | metal ion binding |
A | 0051879 | molecular_function | Hsp90 protein binding |
A | 0140297 | molecular_function | DNA-binding transcription factor binding |
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 | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:19053282 |
Chain | Residue | Details |
A | HIS143 |
site_id | SWS_FT_FI2 |
Number of Residues | 3 |
Details | BINDING: BINDING => ECO:0000269|PubMed:19053282 |
Chain | Residue | Details |
A | ASP101 | |
A | GLY151 | |
A | TYR306 |
site_id | SWS_FT_FI3 |
Number of Residues | 3 |
Details | BINDING: BINDING => ECO:0000269|PubMed:17721440 |
Chain | Residue | Details |
A | ASP178 | |
A | HIS180 | |
A | ASP267 |
site_id | SWS_FT_FI4 |
Number of Residues | 1 |
Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:15242608 |
Chain | Residue | Details |
A | SER39 |