5D1D
Crystal structure of P91L-Y306F HDAC8 in complex with a tetrapeptide substrate
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 | 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 |
| 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 | 0031507 | biological_process | heterochromatin formation |
| 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 | 0046872 | molecular_function | metal ion binding |
| B | 0051879 | molecular_function | Hsp90 protein binding |
| B | 0140297 | molecular_function | DNA-binding transcription factor binding |
| B | 0141221 | molecular_function | histone deacetylase activity, hydrolytic mechanism |
| 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 | 5 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | ASP178 |
| A | HIS180 |
| A | ASP267 |
| A | HOH507 |
| C | ALY5 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue K A 402 |
| Chain | Residue |
| A | LEU200 |
| A | ASP176 |
| A | ASP178 |
| A | HIS180 |
| A | SER199 |
| 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 | HOH524 |
| A | HOH576 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue ZN B 401 |
| Chain | Residue |
| B | ASP178 |
| B | HIS180 |
| B | ASP267 |
| B | HOH510 |
| D | ALY5 |
| site_id | AC5 |
| 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 | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue K B 403 |
| Chain | Residue |
| B | PHE189 |
| B | THR192 |
| B | VAL195 |
| B | TYR225 |
| B | HOH502 |
| B | HOH519 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for Di-peptide ACE C 1 and ARG C 2 |
| Chain | Residue |
| A | ILE94 |
| A | GLU148 |
| C | HIS3 |
| site_id | AC8 |
| Number of Residues | 15 |
| Details | binding site for Di-peptide HIS C 3 and ALY C 4 |
| Chain | Residue |
| A | ASP101 |
| A | PHE208 |
| A | PRO209 |
| A | HOH530 |
| B | PRO273 |
| B | ASN307 |
| B | LEU308 |
| B | ALA309 |
| B | HOH535 |
| C | ACE1 |
| C | ARG2 |
| C | ALY5 |
| C | MCM6 |
| C | HOH101 |
| C | HOH102 |
| site_id | AC9 |
| Number of Residues | 21 |
| Details | binding site for residues ALY C 4 and ALY C 5 |
| Chain | Residue |
| A | ASP101 |
| A | TRP141 |
| A | HIS143 |
| A | GLY151 |
| A | PHE152 |
| A | HIS180 |
| A | PHE208 |
| A | ASP267 |
| A | GLY304 |
| A | PHE306 |
| A | ZN401 |
| A | HOH507 |
| A | HOH530 |
| A | HOH577 |
| B | PRO273 |
| B | ASN307 |
| B | LEU308 |
| B | ALA309 |
| B | HOH535 |
| C | HIS3 |
| C | MCM6 |
| site_id | AD1 |
| Number of Residues | 19 |
| Details | binding site for residues ALY C 5 and MCM C 6 |
| Chain | Residue |
| A | LYS33 |
| A | TYR100 |
| A | ASP101 |
| A | TRP141 |
| A | HIS143 |
| A | GLY151 |
| A | PHE152 |
| A | HIS180 |
| A | PHE208 |
| A | ASP267 |
| A | GLY304 |
| A | PHE306 |
| A | ZN401 |
| A | HOH507 |
| A | HOH577 |
| B | PHE152 |
| B | PRO273 |
| C | ALY4 |
| D | MCM6 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for Di-peptide ACE D 1 and ARG D 2 |
| Chain | Residue |
| B | GLU148 |
| D | HIS3 |
| site_id | AD3 |
| Number of Residues | 17 |
| Details | binding site for Di-peptide HIS D 3 and ALY D 4 |
| Chain | Residue |
| B | ASP101 |
| B | PHE208 |
| B | PRO209 |
| B | HOH534 |
| D | ACE1 |
| D | ARG2 |
| D | ALY5 |
| D | MCM6 |
| D | HOH101 |
| D | HOH103 |
| A | PRO273 |
| A | ASN307 |
| A | LEU308 |
| A | ALA309 |
| A | ALA339 |
| A | HOH573 |
| B | TYR100 |
| site_id | AD4 |
| Number of Residues | 22 |
| Details | binding site for residues ALY D 4 and ALY D 5 |
| Chain | Residue |
| A | PRO273 |
| A | ASN307 |
| A | LEU308 |
| A | ALA309 |
| A | ALA339 |
| A | HOH573 |
| B | TYR100 |
| B | ASP101 |
| B | TRP141 |
| B | GLY151 |
| B | PHE152 |
| B | HIS180 |
| B | PHE208 |
| B | ASP267 |
| B | GLY304 |
| B | PHE306 |
| B | ZN401 |
| B | HOH510 |
| D | HIS3 |
| D | MCM6 |
| D | HOH101 |
| D | HOH102 |
| site_id | AD5 |
| Number of Residues | 18 |
| Details | binding site for residues ALY D 5 and MCM D 6 |
| Chain | Residue |
| A | PHE152 |
| A | PRO273 |
| B | LYS33 |
| B | TYR100 |
| B | ASP101 |
| B | TRP141 |
| B | GLY151 |
| B | PHE152 |
| B | HIS180 |
| B | PHE208 |
| B | ASP267 |
| B | GLY304 |
| B | PHE306 |
| B | ZN401 |
| B | HOH510 |
| C | MCM6 |
| D | ALY4 |
| D | HOH102 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 310 |
| Details | Region: {"description":"Histone deacetylase"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"19053282","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19053282","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"17721440","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"15242608","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
