3MZ4
Crystal structure of D101L Mn2+ HDAC8 complexed with M344
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 | 6 |
| Details | BINDING SITE FOR RESIDUE MN A 390 |
| Chain | Residue |
| A | ASP178 |
| A | HIS180 |
| A | ASP267 |
| A | HOH469 |
| A | HOH470 |
| A | B3N501 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K A 391 |
| Chain | Residue |
| A | SER199 |
| A | LEU200 |
| A | ASP176 |
| A | ASP178 |
| A | HIS180 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K A 392 |
| Chain | Residue |
| A | PHE189 |
| A | THR192 |
| A | VAL195 |
| A | TYR225 |
| A | HOH397 |
| A | HOH413 |
| site_id | AC4 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE B3N A 501 |
| Chain | Residue |
| A | LEU101 |
| A | HIS142 |
| A | HIS143 |
| A | ASP178 |
| A | HIS180 |
| A | PHE208 |
| A | ASP267 |
| A | TYR306 |
| A | MN390 |
| A | HOH469 |
| A | HOH470 |
| A | HOH562 |
| A | GOL705 |
| B | LEU101 |
| B | GLY151 |
| B | PHE152 |
| B | HIS180 |
| B | PHE208 |
| B | MET274 |
| B | TYR306 |
| site_id | AC5 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL A 705 |
| Chain | Residue |
| A | GLY140 |
| A | TRP141 |
| A | HIS143 |
| A | GLY151 |
| A | GLY303 |
| A | GLY304 |
| A | TYR306 |
| A | HOH469 |
| A | HOH470 |
| A | B3N501 |
| B | B3N501 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN B 390 |
| Chain | Residue |
| B | ASP178 |
| B | HIS180 |
| B | ASP267 |
| B | B3N501 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 391 |
| Chain | Residue |
| B | ASP176 |
| B | ASP178 |
| B | HIS180 |
| B | SER199 |
| B | LEU200 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K B 392 |
| Chain | Residue |
| B | PHE189 |
| B | THR192 |
| B | VAL195 |
| B | TYR225 |
| B | HOH393 |
| B | HOH401 |
| site_id | AC9 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE B3N B 501 |
| Chain | Residue |
| A | LEU101 |
| A | PHE152 |
| A | HIS180 |
| A | PHE208 |
| A | MET274 |
| A | TYR306 |
| A | GOL705 |
| B | LEU101 |
| B | HIS142 |
| B | HIS143 |
| B | ASP178 |
| B | HIS180 |
| B | PHE208 |
| B | ASP267 |
| B | GLY304 |
| B | TYR306 |
| B | MN390 |
| B | GOL706 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 706 |
| Chain | Residue |
| B | TRP141 |
| B | GLY151 |
| B | PHE152 |
| B | GLY303 |
| B | TYR306 |
| B | B3N501 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| 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_FI2 |
| Number of Residues | 6 |
| Details | Binding site: {"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":"17721440","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"15242608","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
