4RN1
Crystal structure of S39D HDAC8 in complex with a largazole analogue.
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 |
| B | 0000118 | cellular_component | histone deacetylase complex |
| B | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| B | 0000228 | cellular_component | nuclear chromosome |
| B | 0004407 | molecular_function | histone deacetylase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005694 | cellular_component | chromosome |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006325 | biological_process | chromatin organization |
| B | 0007064 | biological_process | mitotic sister chromatid cohesion |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0030544 | molecular_function | Hsp70 protein binding |
| B | 0031397 | biological_process | negative regulation of protein ubiquitination |
| B | 0031647 | biological_process | regulation of protein stability |
| B | 0032204 | biological_process | regulation of telomere maintenance |
| B | 0033558 | molecular_function | protein lysine deacetylase activity |
| B | 0040029 | biological_process | epigenetic regulation of gene expression |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051879 | molecular_function | Hsp90 protein binding |
| B | 0140297 | molecular_function | DNA-binding transcription factor binding |
| B | 0160008 | molecular_function | protein decrotonylase activity |
| B | 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 |
| A | L8G404 |
| 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 | HOH501 |
| A | HOH503 |
| site_id | AC4 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE L8G A 404 |
| Chain | Residue |
| A | TYR100 |
| A | HIS143 |
| A | PHE152 |
| A | HIS180 |
| A | PHE208 |
| A | TYR306 |
| A | ZN401 |
| A | IMD405 |
| A | HOH671 |
| A | HOH672 |
| A | HOH673 |
| B | LYS33 |
| B | PRO273 |
| B | TYR306 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE IMD A 405 |
| Chain | Residue |
| A | PRO273 |
| A | L8G404 |
| B | MET274 |
| B | L8G404 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 406 |
| Chain | Residue |
| A | LYS289 |
| A | TYR317 |
| A | GLY320 |
| A | LYS325 |
| A | HOH607 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 401 |
| Chain | Residue |
| B | ASP178 |
| B | HIS180 |
| B | ASP267 |
| B | L8G404 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 402 |
| Chain | Residue |
| B | ASP176 |
| B | ASP178 |
| B | HIS180 |
| B | SER199 |
| B | LEU200 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K B 403 |
| Chain | Residue |
| B | PHE189 |
| B | THR192 |
| B | VAL195 |
| B | TYR225 |
| B | HOH501 |
| B | HOH503 |
| site_id | BC1 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE L8G B 404 |
| Chain | Residue |
| A | LYS33 |
| A | PRO273 |
| A | TYR306 |
| A | IMD405 |
| B | LYS33 |
| B | HIS143 |
| B | PHE152 |
| B | HIS180 |
| B | PHE208 |
| B | ASP267 |
| B | TYR306 |
| B | ZN401 |
| B | HOH574 |
| B | HOH634 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:19053282 |
| Chain | Residue | Details |
| A | HIS143 | |
| B | HIS143 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19053282 |
| Chain | Residue | Details |
| A | ASP101 | |
| A | GLY151 | |
| A | TYR306 | |
| B | ASP101 | |
| B | GLY151 | |
| B | TYR306 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17721440 |
| Chain | Residue | Details |
| A | ASP178 | |
| A | HIS180 | |
| A | ASP267 | |
| B | ASP178 | |
| B | HIS180 | |
| B | ASP267 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:15242608 |
| Chain | Residue | Details |
| A | ASP39 | |
| B | ASP39 |
